diff --git a/SequenceAnalysis/resources/web/SequenceAnalysis/panel/VariantScatterGatherPanel.js b/SequenceAnalysis/resources/web/SequenceAnalysis/panel/VariantScatterGatherPanel.js
index 5b0204a11..3b8daa105 100644
--- a/SequenceAnalysis/resources/web/SequenceAnalysis/panel/VariantScatterGatherPanel.js
+++ b/SequenceAnalysis/resources/web/SequenceAnalysis/panel/VariantScatterGatherPanel.js
@@ -3,6 +3,7 @@ Ext4.define('SequenceAnalysis.panel.VariantScatterGatherPanel', {
     alias: 'widget.sequenceanalysis-variantscattergatherpanel',
 
     defaultFieldWidth: null,
+    labelWidth: null,
 
     initComponent: function (){
         Ext4.apply(this, {
diff --git a/SequenceAnalysis/resources/web/SequenceAnalysis/window/LiftoverWindow.js b/SequenceAnalysis/resources/web/SequenceAnalysis/window/LiftoverWindow.js
index 8398fc47a..8b30bf513 100644
--- a/SequenceAnalysis/resources/web/SequenceAnalysis/window/LiftoverWindow.js
+++ b/SequenceAnalysis/resources/web/SequenceAnalysis/window/LiftoverWindow.js
@@ -56,7 +56,7 @@ Ext4.define('SequenceAnalysis.window.LiftoverWindow', {
                                         containerPath: containerPath,
                                         dataRegionName: dataRegionName,
                                         outputFileIds: checked,
-                                        libraryId: distinctGenomes.length == 1 ? distinctGenomes[0] : null,
+                                        libraryId: distinctGenomes.length === 1 ? distinctGenomes[0] : null,
                                         toolParameters: results.toolParameters
                                     }).show();
                                 }
@@ -71,7 +71,7 @@ Ext4.define('SequenceAnalysis.window.LiftoverWindow', {
     initComponent: function(){
         Ext4.apply(this, {
             bodyStyle: 'padding: 5px;',
-            width: 500,
+            width: 600,
             modal: true,
             title: 'Liftover File(s) To Alternate Genome',
             items: [{
@@ -117,12 +117,17 @@ Ext4.define('SequenceAnalysis.window.LiftoverWindow', {
                 itemId: 'useBcfTools',
                 checked: true,
                 fieldLabel: 'Use bcftools'
-            },{
+            }, {
                 xtype: 'checkbox',
-                itemId: 'doNotRetainUnmapped',
+                itemId: 'retainUnmapped',
                 checked: false,
-                fieldLabel: 'Do Not Retain Unmapped'
-            }].concat(SequenceAnalysis.window.OutputHandlerWindow.getCfgForToolParameters(this.toolParameters)),
+                fieldLabel: 'Retain Unmapped Variants'
+            }].concat(SequenceAnalysis.window.OutputHandlerWindow.getCfgForToolParameters(this.toolParameters)).concat([{
+                xtype: 'sequenceanalysis-variantscattergatherpanel',
+                defaultFieldWidth: 500,
+                labelWidth: 200,
+                bodyStyle: ''
+            }]),
             buttons: [{
                 text: 'Submit',
                 handler: this.onSubmit,
@@ -158,21 +163,23 @@ Ext4.define('SequenceAnalysis.window.LiftoverWindow', {
             params.pct = this.down('#pctField').getValue();
         }
 
-        if (this.down('#dropGenotypes').getValue()){
-            params.dropGenotypes = this.down('#dropGenotypes').getValue();
-        }
+        params.dropGenotypes = !!this.down('#dropGenotypes').getValue();
+        params.useBcfTools = !!this.down('#useBcfTools').getValue();
+        params.retainUnmapped = !!this.down('#retainUnmapped').getValue();
 
-        if (this.down('#useBcfTools').getValue()){
-            params.useBcfTools = this.down('#useBcfTools').getValue();
-        }
+        Ext4.Array.forEach(this.down('sequenceanalysis-variantscattergatherpanel').query('field'), function(field){
+            params[field.name] = field.getValue();
+        }, this);
 
-        if (this.down('#doNotRetainUnmapped').getValue()){
-            params.doNotRetainUnmapped = this.down('#doNotRetainUnmapped').getValue();
+        var actionName = 'runSequenceHandler';
+        if (params.scatterGatherMethod && params.scatterGatherMethod !== 'none') {
+            params.scatterGather = true;
+            actionName = 'runVariantProcessing';
         }
 
         Ext4.Msg.wait('Saving...');
         LABKEY.Ajax.request({
-            url: LABKEY.ActionURL.buildURL('sequenceanalysis', 'runSequenceHandler', this.containerPath),
+            url: LABKEY.ActionURL.buildURL('sequenceanalysis', actionName, this.containerPath),
             jsonData: {
                 handlerClass: 'org.labkey.sequenceanalysis.analysis.LiftoverHandler',
                 outputFileIds: this.outputFileIds,
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/GenotypeGVCFHandler.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/GenotypeGVCFHandler.java
index 1968a55d8..82d19d3dd 100644
--- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/GenotypeGVCFHandler.java
+++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/GenotypeGVCFHandler.java
@@ -717,7 +717,9 @@ private void processOneInput(JobContext ctx, PipelineJob job, ReferenceGenome ge
                         toolParams.add(interval.getContig() + ":" + interval.getStart() + "-" + interval.getEnd());
                     });
                 }
-                toolParams.add("--only-output-calls-starting-in-intervals");
+
+                toolParams.add("--variant-output-filtering");
+                toolParams.add("STARTS_IN");
             }
 
             if (ctx.getParams().optBoolean("variantCalling.GenotypeGVCFs.disableFileLocking", false))
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/LiftoverHandler.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/LiftoverHandler.java
index 93189cde9..5b1cda83b 100644
--- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/LiftoverHandler.java
+++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/LiftoverHandler.java
@@ -30,20 +30,21 @@
 import org.labkey.api.sequenceanalysis.pipeline.SequenceOutputHandler;
 import org.labkey.api.sequenceanalysis.pipeline.SequencePipelineService;
 import org.labkey.api.sequenceanalysis.pipeline.VariantProcessingStep;
+import org.labkey.api.sequenceanalysis.run.LiftoverBcfToolsWrapper;
 import org.labkey.api.sequenceanalysis.run.SelectVariantsWrapper;
 import org.labkey.api.util.FileType;
-import org.labkey.api.util.FileUtil;
 import org.labkey.api.view.ActionURL;
 import org.labkey.api.writer.PrintWriters;
 import org.labkey.sequenceanalysis.SequenceAnalysisModule;
 import org.labkey.sequenceanalysis.pipeline.ProcessVariantsHandler;
-import org.labkey.api.sequenceanalysis.run.LiftoverBcfToolsWrapper;
+import org.labkey.sequenceanalysis.pipeline.SequenceOutputHandlerJob;
 import org.labkey.sequenceanalysis.run.util.LiftoverVcfWrapper;
 import org.labkey.sequenceanalysis.util.SequenceUtil;
 
 import java.io.File;
 import java.io.IOException;
 import java.text.NumberFormat;
+import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Date;
 import java.util.LinkedHashSet;
@@ -52,11 +53,10 @@
 /**
  * Created by bimber on 8/26/2014.
  */
-public class LiftoverHandler implements SequenceOutputHandler<SequenceOutputHandler.SequenceOutputProcessor>, VariantProcessingStep.SupportsScatterGather
+public class LiftoverHandler implements SequenceOutputHandler<SequenceOutputHandler.SequenceOutputProcessor>, VariantProcessingStep.SupportsScatterGather, SequenceOutputHandler.TracksVCF
 {
-    private final FileType _bedFileType = new FileType(".bed", false);
-    //private FileType _gffFileType = new FileType("gff", false);
-    private final FileType _vcfFileType = new FileType(Arrays.asList(".vcf", ".bcf"), ".vcf", false, FileType.gzSupportLevel.SUPPORT_GZ);
+    private static final FileType _bedFileType = new FileType(".bed", false);
+    private static final FileType _vcfFileType = new FileType(Arrays.asList(".vcf", ".bcf"), ".vcf", false, FileType.gzSupportLevel.SUPPORT_GZ);
 
     public LiftoverHandler()
     {
@@ -131,6 +131,30 @@ public boolean canProcess(SequenceOutputFile f)
                 _vcfFileType.isType(f.getFile()));
     }
 
+    private static File getUnmappedOutputFile(File liftedVcfFile)
+    {
+        return new File(liftedVcfFile.getParentFile(), liftedVcfFile.getName().replaceAll(".lifted-", ".unmapped-"));
+    }
+
+    private static String getOutputExtension(File inputFile)
+    {
+        String ext = null;
+        if (_bedFileType.isType(inputFile))
+        {
+            ext = ".bed";
+        }
+        else if (_vcfFileType.isType(inputFile))
+        {
+            ext = ".vcf.gz";
+        }
+        else
+        {
+            throw new UnsupportedOperationException("Unsupported file type: " + inputFile.getName());
+        }
+
+        return ext;
+    }
+
     @Override
     public SequenceOutputProcessor getProcessor()
     {
@@ -140,7 +164,7 @@ public SequenceOutputProcessor getProcessor()
     @Override
     public boolean doSplitJobs()
     {
-        return false;
+        return true;
     }
 
     public class Processor implements SequenceOutputProcessor
@@ -175,150 +199,123 @@ public void processFilesRemote(List<SequenceOutputFile> inputFiles, JobContext c
             PipelineJob job = ctx.getJob();
             JSONObject params = ctx.getParams();
 
+            List<Interval> intervals = ProcessVariantsHandler.getIntervals(ctx);
+
             boolean dropGenotypes = params.optBoolean("dropGenotypes", false);
             boolean useBcfTools = params.optBoolean("useBcfTools", false);
-            boolean doNotRetainUnmapped = params.optBoolean("doNotRetainUnmapped", false);
-            if (!doNotRetainUnmapped && !useBcfTools)
-            {
-                ctx.getLogger().debug("Picard LiftoverVcf requires an output file for rejected sites, so setting doNotRetainUnmapped to true");
-                doNotRetainUnmapped = true;
-            }
+            boolean retainUnmapped = params.optBoolean("retainUnmapped", false);
 
             int chainFileId = params.getInt("chainFileId");
             File chainFile = ctx.getSequenceSupport().getCachedData(chainFileId);
             int targetGenomeId = params.getInt("targetGenomeId");
 
-            for (SequenceOutputFile f : inputFiles)
+            if (inputFiles.size() > 1)
             {
-                job.getLogger().info("processing output: " + f.getFile().getName());
+                throw new PipelineJobException("Expected single input file");
+            }
+
+            SequenceOutputFile f = inputFiles.get(0);
+            job.getLogger().info("processing output: " + f.getFile().getName());
 
-                RecordedAction action = new RecordedAction(getName());
-                action.setStartTime(new Date());
+            RecordedAction action = new RecordedAction(getName());
+            action.setStartTime(new Date());
 
-                boolean isGzip = f.getFile().getPath().toLowerCase().endsWith("gz");
-                int dots = isGzip ? 2 : 1;
-                String baseName = FileUtil.getBaseName(f.getFile(), dots);
+            double pct = params.has("pct") ? params.getDouble("pct") : 0.95;
+            job.getLogger().info("using minimum percent match: " + pct);
 
-                double pct = params.has("pct") ? params.getDouble("pct") : 0.95;
-                job.getLogger().info("using minimum percent match: " + pct);
+            action.addInput(f.getFile(), "Input File");
+            action.addInput(chainFile, "Chain File");
 
-                action.addInput(f.getFile(), "Input File");
-                action.addInput(chainFile, "Chain File");
+            File outDir = ((FileAnalysisJobSupport) job).getAnalysisDirectory();
+            String baseName = SequenceAnalysisService.get().getUnzippedBaseName(f.getFile().getName());
+            File lifted = new File(outDir, baseName + ".lifted-" + targetGenomeId + getOutputExtension(f.getFile()));
+            File unmappedOutput = retainUnmapped ? getUnmappedOutputFile(lifted) : null;
 
-                File outDir = ((FileAnalysisJobSupport) job).getAnalysisDirectory();
-                String ext = null;
+            try
+            {
                 if (_bedFileType.isType(f.getFile()))
                 {
-                    ext = ".bed";
+                    liftOverBed(chainFile, f.getFile(), lifted, unmappedOutput, job, pct);
                 }
                 else if (_vcfFileType.isType(f.getFile()))
                 {
-                    ext = ".vcf.gz";
-                }
-                else
-                {
-                    throw new UnsupportedOperationException("Unsupported file type: " + f.getFile().getName());
+                    ReferenceGenome targetGenome = ctx.getSequenceSupport().getCachedGenome(targetGenomeId);
+                    ReferenceGenome sourceGenome = ctx.getSequenceSupport().getCachedGenome(f.getLibrary_id());
+                    liftOverVcf(ctx, targetGenome, sourceGenome, chainFile, f.getFile(), lifted, unmappedOutput, job, pct, dropGenotypes, useBcfTools, intervals);
                 }
+            }
+            catch (Exception e)
+            {
+                throw new PipelineJobException(e);
+            }
 
-                File lifted = new File(outDir, baseName + ".lifted-" + targetGenomeId + ext);
-                File unmappedOutput = doNotRetainUnmapped ? null : new File(outDir, baseName + ".unmapped-" + targetGenomeId + ext);
+            job.getLogger().info("adding outputs");
+            action.addOutput(lifted, "Lifted Features", lifted.exists(), true);
+            if (lifted.exists())
+            {
+                job.getLogger().info("adding lifted features: " + lifted.getName());
+
+                SequenceOutputFile so1 = new SequenceOutputFile();
+                so1.setName(f.getName() + " (lifted)");
+                so1.setDescription("Contains features from " + f.getName() + " after liftover");
+                so1.setFile(lifted);
+                so1.setLibrary_id(targetGenomeId);
+                so1.setReadset(f.getReadset());
+                so1.setAnalysis_id(f.getAnalysis_id());
+                so1.setCategory(f.getCategory());
+                so1.setContainer(job.getContainerId());
+                so1.setCreated(new Date());
+                so1.setModified(new Date());
+
+                ctx.addSequenceOutput(so1);
+            }
 
-                try
-                {
-                    if (_bedFileType.isType(f.getFile()))
-                    {
-                        liftOverBed(chainFile, f.getFile(), lifted, unmappedOutput, job, pct);
-                    }
-                    else if (_vcfFileType.isType(f.getFile()))
-                    {
-                        ReferenceGenome targetGenome = ctx.getSequenceSupport().getCachedGenome(targetGenomeId);
-                        ReferenceGenome sourceGenome = ctx.getSequenceSupport().getCachedGenome(f.getLibrary_id());
-                        liftOverVcf(ctx, targetGenome, sourceGenome, chainFile, f.getFile(), lifted, unmappedOutput, job, pct, dropGenotypes, useBcfTools);
-                    }
-                }
-                catch (Exception e)
-                {
-                    throw new PipelineJobException(e);
-                }
+            if (unmappedOutput == null)
+            {
+                // skip
+            }
+            else if (!unmappedOutput.exists())
+            {
+                job.getLogger().info("no unmapped intervals");
+            }
+            else if (!SequenceUtil.hasLineCount(unmappedOutput))
+            {
+                job.getLogger().info("no unmapped intervals");
+                unmappedOutput.delete();
+            }
+            else
+            {
+                job.getLogger().info("adding unmapped features: " + unmappedOutput.getName());
 
-                job.getLogger().info("adding outputs");
-                action.addOutput(lifted, "Lifted Features", lifted.exists(), true);
-                if (lifted.exists())
-                {
-                    job.getLogger().info("adding lifted features: " + lifted.getName());
-
-                    SequenceOutputFile so1 = new SequenceOutputFile();
-                    so1.setName(f.getName() + " (lifted)");
-                    so1.setDescription("Contains features from " + f.getName() + " after liftover");
-                    //ExpData liftedData = ExperimentService.get().createData(job.getContainer(), new DataType("Liftover Output"));
-                    //liftedData.setDataFileURI(lifted.toURI());
-                    //liftedData.setName(lifted.getName());
-                    //liftedData.save(job.getUser());
-                    //so1.setDataId(liftedData.getRowId());
-                    so1.setFile(lifted);
-                    so1.setLibrary_id(targetGenomeId);
-                    so1.setReadset(f.getReadset());
-                    so1.setAnalysis_id(f.getAnalysis_id());
-                    so1.setCategory(f.getCategory());
-                    so1.setContainer(job.getContainerId());
-                    so1.setCreated(new Date());
-                    so1.setModified(new Date());
-
-                    ctx.addSequenceOutput(so1);
-                }
+                action.addOutput(unmappedOutput, "Unmapped features", false, true);
 
-                if (unmappedOutput == null)
-                {
-                    // skip
-                }
-                else if (!unmappedOutput.exists())
-                {
-                    job.getLogger().info("no unmapped intervals");
-                }
-                else if (!SequenceUtil.hasLineCount(unmappedOutput))
-                {
-                    job.getLogger().info("no unmapped intervals");
-                    unmappedOutput.delete();
-                }
-                else
-                {
-                    job.getLogger().info("adding unmapped features: " + unmappedOutput.getName());
-
-                    action.addOutput(unmappedOutput, "Unmapped features", false, true);
-
-                    SequenceOutputFile so2 = new SequenceOutputFile();
-                    so2.setName(f.getName() + " (lifted/unmapped)");
-                    so2.setDescription("Contains the unmapped features after attempted liftover of " + f.getName());
-
-                    //ExpData unmappedData = ExperimentService.get().createData(job.getContainer(), new DataType("Liftover Output"));
-                    //unmappedData.setName(unmappedOutput.getName());
-                    //unmappedData.setDataFileURI(unmappedOutput.toURI());
-                    //unmappedData.save(job.getUser());
-                    //so2.setDataId(unmappedData.getRowId());
-                    so2.setFile(unmappedOutput);
-                    so2.setLibrary_id(f.getLibrary_id());
-                    so2.setReadset(f.getReadset());
-                    so2.setAnalysis_id(f.getAnalysis_id());
-                    so2.setCategory(f.getCategory());
-                    so2.setContainer(job.getContainerId());
-                    so2.setCreated(new Date());
-                    so2.setModified(new Date());
-
-                    ctx.addSequenceOutput(so2);
-                }
+                SequenceOutputFile so2 = new SequenceOutputFile();
+                so2.setName(f.getName() + " (lifted/unmapped)");
+                so2.setDescription("Contains the unmapped features after attempted liftover of " + f.getName());
+
+                so2.setFile(unmappedOutput);
+                so2.setLibrary_id(f.getLibrary_id());
+                so2.setReadset(f.getReadset());
+                so2.setAnalysis_id(f.getAnalysis_id());
+                so2.setCategory(f.getCategory());
+                so2.setContainer(job.getContainerId());
+                so2.setCreated(new Date());
+                so2.setModified(new Date());
 
-                action.setEndTime(new Date());
-                ctx.addActions(action);
+                ctx.addSequenceOutput(so2);
             }
+
+            action.setEndTime(new Date());
+            ctx.addActions(action);
         }
     }
 
-    public void liftOverVcf(JobContext ctx, ReferenceGenome targetGenome, ReferenceGenome sourceGenome, File chain, File input, File output, @Nullable File unmappedOutput, PipelineJob job, double pct, boolean dropGenotypes, boolean useBcfTools) throws IOException, PipelineJobException
+    public void liftOverVcf(JobContext ctx, ReferenceGenome targetGenome, ReferenceGenome sourceGenome, File chain, File input, File output, @Nullable File unmappedOutput, PipelineJob job, double pct, boolean dropGenotypes, boolean useBcfTools, @Nullable List<Interval> intervals) throws IOException, PipelineJobException
     {
         File currentVCF = input;
-        if (dropGenotypes)
+        if (dropGenotypes || intervals != null)
         {
-            ctx.getLogger().info("creating VCF wihtout genotypes");
+            ctx.getLogger().info("subsetting VCF");
             File outputFile = new File(output.getParentFile(), SequenceAnalysisService.get().getUnzippedBaseName(currentVCF.getName()) + ".noGenotypes.vcf.gz");
             if (new File(outputFile.getPath() + ".tbi").exists())
             {
@@ -326,8 +323,28 @@ public void liftOverVcf(JobContext ctx, ReferenceGenome targetGenome, ReferenceG
             }
             else
             {
+                List<String> extraArgs = new ArrayList<>();
+                if (dropGenotypes)
+                {
+                    extraArgs.add("--sites-only-vcf-output");
+                }
+
+                if (intervals != null)
+                {
+                    intervals.forEach(interval -> {
+                        extraArgs.add("-L");
+                        extraArgs.add(interval.getContig() + ":" + interval.getStart() + "-" + interval.getEnd());
+                    });
+
+                    extraArgs.add("--variant-output-filtering");
+                    extraArgs.add("STARTS_IN");
+                }
+
                 SelectVariantsWrapper wrapper = new SelectVariantsWrapper(job.getLogger());
-                wrapper.execute(sourceGenome.getWorkingFastaFile(), currentVCF, outputFile, List.of("--sites-only-vcf-output"));
+                wrapper.execute(sourceGenome.getWorkingFastaFile(), currentVCF, outputFile, extraArgs);
+
+                ctx.getFileManager().addIntermediateFile(outputFile);
+                ctx.getFileManager().addIntermediateFile(new File(outputFile.getPath() + ".tbi"));
             }
             currentVCF = outputFile;
 
@@ -344,8 +361,21 @@ public void liftOverVcf(JobContext ctx, ReferenceGenome targetGenome, ReferenceG
         }
         else
         {
+            File unmappedOutputFile = unmappedOutput;
+            if (unmappedOutputFile == null)
+            {
+                unmappedOutputFile = new File(currentVCF.getParentFile(), "liftoverRejects.vcf.gz");
+            }
+
             LiftoverVcfWrapper wrapper = new LiftoverVcfWrapper(job.getLogger());
             wrapper.doLiftover(currentVCF, chain, targetGenome.getWorkingFastaFile(), unmappedOutput, output, pct);
+
+            if (unmappedOutput == null)
+            {
+                ctx.getLogger().debug("Deleting liftover rejects VCF");
+                new File(unmappedOutputFile.getPath() + ".tbi").delete();
+                unmappedOutputFile.delete();
+            }
         }
 
         Long mapped = null;
@@ -358,7 +388,7 @@ public void liftOverVcf(JobContext ctx, ReferenceGenome targetGenome, ReferenceG
             SequenceAnalysisService.get().ensureVcfIndex(output, job.getLogger());
         }
 
-        Long unmapped = 0L;
+        long unmapped = 0L;
         if (unmappedOutput != null && unmappedOutput.exists())
         {
             String unmappedStr = ProcessVariantsHandler.getVCFLineCount(unmappedOutput, job.getLogger(), false, true);
@@ -370,11 +400,32 @@ public void liftOverVcf(JobContext ctx, ReferenceGenome targetGenome, ReferenceG
 
         if (mapped != null)
         {
-            Double fraction = (double)mapped / (mapped + unmapped);
+            double fraction = (double)mapped / (mapped + unmapped);
             job.getLogger().info("fraction mapped of total: " + fraction);
         }
     }
 
+    @Override
+    public File getScatterJobOutput(JobContext ctx) throws PipelineJobException
+    {
+        if (ctx.getJob() instanceof SequenceOutputHandlerJob sj)
+        {
+            SequenceOutputFile so = sj.getFiles().get(0);
+
+            return ProcessVariantsHandler.getScatterOutputByCategory(ctx, so.getCategory());
+        }
+        else
+        {
+            throw new IllegalStateException("Expected job to be instanceof SequenceOutputHandlerJob , was " + ctx.getJob().getClass().getName());
+        }
+    }
+
+    @Override
+    public SequenceOutputFile createFinalSequenceOutput(PipelineJob job, File processed, List<SequenceOutputFile> inputFiles) throws PipelineJobException
+    {
+        return ProcessVariantsHandler.createSequenceOutput(job, processed, inputFiles, inputFiles.get(0).getCategory());
+    }
+
     public void liftOverBed(File chain, File input, File output, @Nullable File unmappedOutput, PipelineJob job, double pct) throws IOException, PipelineJobException
     {
         LiftOver lo = new LiftOver(chain);
@@ -420,4 +471,50 @@ public void liftOverBed(File chain, File input, File output, @Nullable File unma
         //sort resulting file
         SequenceUtil.sortROD(output, job.getLogger(), 2);
     }
+
+    @Override
+    public void performAdditionalMergeTasks(JobContext ctx, PipelineJob job, ReferenceGenome genome, List<File> orderedScatterOutputs, List<String> orderedJobDirs) throws PipelineJobException
+    {
+        boolean retainUnmapped = ctx.getParams().optBoolean("retainUnmapped", true);
+        if (retainUnmapped)
+        {
+            job.getLogger().info("Merging liftOver reject VCFs");
+            List<File> toConcat = orderedScatterOutputs.stream().map(vcfFile -> {
+                File f = getUnmappedOutputFile(vcfFile);
+                if (!f.exists())
+                {
+                    throw new IllegalStateException("Missing file: " + f.getPath());
+                }
+
+                ctx.getFileManager().addIntermediateFile(f);
+                ctx.getFileManager().addIntermediateFile(new File(f.getPath() + ".tbi"));
+
+                return f;
+            }).toList();
+
+            job.getLogger().debug("Total VCFs to merge: " + toConcat.size());
+            if (toConcat.isEmpty())
+            {
+                throw new PipelineJobException("No unmapped VCF found");
+            }
+
+            File combined = getUnmappedOutputFile(orderedScatterOutputs.get(0));
+            File combinedIdx = new File(combined.getPath() + ".tbi");
+            if (combinedIdx.exists())
+            {
+                job.getLogger().info("VCF exists, will not recreate: " + combined.getPath());
+            }
+            else
+            {
+                combined = SequenceAnalysisService.get().combineVcfs(toConcat, combined, genome, job.getLogger(), true, null);
+            }
+
+            SequenceOutputFile so = new SequenceOutputFile();
+            so.setName(orderedScatterOutputs.get(0).getName() + ": Lifted/Unmapped");
+            so.setFile(combined);
+            so.setCategory("VCF File");
+            so.setLibrary_id(genome.getGenomeId());
+            ctx.getFileManager().addSequenceOutput(so);
+        }
+    }
 }
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/OrphanFilePipelineJob.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/OrphanFilePipelineJob.java
index 026177561..e6a657190 100644
--- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/OrphanFilePipelineJob.java
+++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/OrphanFilePipelineJob.java
@@ -534,7 +534,7 @@ private void getOrphanFilesForDirectory(Set<Integer> knownExpDatas, Map<URI, Set
                         getJob().getLogger().warn("WARNING: Extremely large log file: " + f.getPath() + ", " + FileUtils.byteCountToDisplaySize(f.length()));
                     }
 
-                    if (f.getName().endsWith(".rds"))
+                    if (f.getName().endsWith(".rds") && !f.getName().endsWith("hashing.rawCounts.rds"))
                     {
                         if (!dataMap.containsKey(f.toURI()))
                         {
diff --git a/jbrowse/package-lock.json b/jbrowse/package-lock.json
index a272bd98a..3938e1886 100644
--- a/jbrowse/package-lock.json
+++ b/jbrowse/package-lock.json
@@ -92,22 +92,21 @@
       }
     },
     "node_modules/@babel/core": {
-      "version": "7.26.8",
-      "resolved": "https://registry.npmjs.org/@babel/core/-/core-7.26.8.tgz",
-      "integrity": "sha512-l+lkXCHS6tQEc5oUpK28xBOZ6+HwaH7YwoYQbLFiYb4nS2/l1tKnZEtEWkD0GuiYdvArf9qBS0XlQGXzPMsNqQ==",
+      "version": "7.26.10",
+      "resolved": "https://registry.npmjs.org/@babel/core/-/core-7.26.10.tgz",
+      "integrity": "sha512-vMqyb7XCDMPvJFFOaT9kxtiRh42GwlZEg1/uIgtZshS5a/8OaduUfCi7kynKgc3Tw/6Uo2D+db9qBttghhmxwQ==",
       "dev": true,
       "dependencies": {
         "@ampproject/remapping": "^2.2.0",
         "@babel/code-frame": "^7.26.2",
-        "@babel/generator": "^7.26.8",
+        "@babel/generator": "^7.26.10",
         "@babel/helper-compilation-targets": "^7.26.5",
         "@babel/helper-module-transforms": "^7.26.0",
-        "@babel/helpers": "^7.26.7",
-        "@babel/parser": "^7.26.8",
-        "@babel/template": "^7.26.8",
-        "@babel/traverse": "^7.26.8",
-        "@babel/types": "^7.26.8",
-        "@types/gensync": "^1.0.0",
+        "@babel/helpers": "^7.26.10",
+        "@babel/parser": "^7.26.10",
+        "@babel/template": "^7.26.9",
+        "@babel/traverse": "^7.26.10",
+        "@babel/types": "^7.26.10",
         "convert-source-map": "^2.0.0",
         "debug": "^4.1.0",
         "gensync": "^1.0.0-beta.2",
@@ -129,12 +128,12 @@
       "dev": true
     },
     "node_modules/@babel/generator": {
-      "version": "7.26.8",
-      "resolved": "https://registry.npmjs.org/@babel/generator/-/generator-7.26.8.tgz",
-      "integrity": "sha512-ef383X5++iZHWAXX0SXQR6ZyQhw/0KtTkrTz61WXRhFM6dhpHulO/RJz79L8S6ugZHJkOOkUrUdxgdF2YiPFnA==",
+      "version": "7.27.0",
+      "resolved": "https://registry.npmjs.org/@babel/generator/-/generator-7.27.0.tgz",
+      "integrity": "sha512-VybsKvpiN1gU1sdMZIp7FcqphVVKEwcuj02x73uvcHE0PTihx1nlBcowYWhDwjpoAXRv43+gDzyggGnn1XZhVw==",
       "dependencies": {
-        "@babel/parser": "^7.26.8",
-        "@babel/types": "^7.26.8",
+        "@babel/parser": "^7.27.0",
+        "@babel/types": "^7.27.0",
         "@jridgewell/gen-mapping": "^0.3.5",
         "@jridgewell/trace-mapping": "^0.3.25",
         "jsesc": "^3.0.2"
@@ -167,12 +166,12 @@
       }
     },
     "node_modules/@babel/helper-compilation-targets": {
-      "version": "7.26.5",
-      "resolved": "https://registry.npmjs.org/@babel/helper-compilation-targets/-/helper-compilation-targets-7.26.5.tgz",
-      "integrity": "sha512-IXuyn5EkouFJscIDuFF5EsiSolseme1s0CZB+QxVugqJLYmKdxI1VfIBOst0SUu4rnk2Z7kqTwmoO1lp3HIfnA==",
+      "version": "7.27.0",
+      "resolved": "https://registry.npmjs.org/@babel/helper-compilation-targets/-/helper-compilation-targets-7.27.0.tgz",
+      "integrity": "sha512-LVk7fbXml0H2xH34dFzKQ7TDZ2G4/rVTOrq9V+icbbadjbVxxeFeDsNHv2SrZeWoA+6ZiTyWYWtScEIW07EAcA==",
       "dev": true,
       "dependencies": {
-        "@babel/compat-data": "^7.26.5",
+        "@babel/compat-data": "^7.26.8",
         "@babel/helper-validator-option": "^7.25.9",
         "browserslist": "^4.24.0",
         "lru-cache": "^5.1.1",
@@ -183,17 +182,17 @@
       }
     },
     "node_modules/@babel/helper-create-class-features-plugin": {
-      "version": "7.25.9",
-      "resolved": "https://registry.npmjs.org/@babel/helper-create-class-features-plugin/-/helper-create-class-features-plugin-7.25.9.tgz",
-      "integrity": "sha512-UTZQMvt0d/rSz6KI+qdu7GQze5TIajwTS++GUozlw8VBJDEOAqSXwm1WvmYEZwqdqSGQshRocPDqrt4HBZB3fQ==",
+      "version": "7.27.0",
+      "resolved": "https://registry.npmjs.org/@babel/helper-create-class-features-plugin/-/helper-create-class-features-plugin-7.27.0.tgz",
+      "integrity": "sha512-vSGCvMecvFCd/BdpGlhpXYNhhC4ccxyvQWpbGL4CWbvfEoLFWUZuSuf7s9Aw70flgQF+6vptvgK2IfOnKlRmBg==",
       "dev": true,
       "dependencies": {
         "@babel/helper-annotate-as-pure": "^7.25.9",
         "@babel/helper-member-expression-to-functions": "^7.25.9",
         "@babel/helper-optimise-call-expression": "^7.25.9",
-        "@babel/helper-replace-supers": "^7.25.9",
+        "@babel/helper-replace-supers": "^7.26.5",
         "@babel/helper-skip-transparent-expression-wrappers": "^7.25.9",
-        "@babel/traverse": "^7.25.9",
+        "@babel/traverse": "^7.27.0",
         "semver": "^6.3.1"
       },
       "engines": {
@@ -204,9 +203,9 @@
       }
     },
     "node_modules/@babel/helper-create-regexp-features-plugin": {
-      "version": "7.26.3",
-      "resolved": "https://registry.npmjs.org/@babel/helper-create-regexp-features-plugin/-/helper-create-regexp-features-plugin-7.26.3.tgz",
-      "integrity": "sha512-G7ZRb40uUgdKOQqPLjfD12ZmGA54PzqDFUv2BKImnC9QIfGhIHKvVML0oN8IUiDq4iRqpq74ABpvOaerfWdong==",
+      "version": "7.27.0",
+      "resolved": "https://registry.npmjs.org/@babel/helper-create-regexp-features-plugin/-/helper-create-regexp-features-plugin-7.27.0.tgz",
+      "integrity": "sha512-fO8l08T76v48BhpNRW/nQ0MxfnSdoSKUJBMjubOAYffsVuGG5qOfMq7N6Es7UJvi7Y8goXXo07EfcHZXDPuELQ==",
       "dev": true,
       "dependencies": {
         "@babel/helper-annotate-as-pure": "^7.25.9",
@@ -221,9 +220,9 @@
       }
     },
     "node_modules/@babel/helper-define-polyfill-provider": {
-      "version": "0.6.3",
-      "resolved": "https://registry.npmjs.org/@babel/helper-define-polyfill-provider/-/helper-define-polyfill-provider-0.6.3.tgz",
-      "integrity": "sha512-HK7Bi+Hj6H+VTHA3ZvBis7V/6hu9QuTrnMXNybfUf2iiuU/N97I8VjB+KbhFF8Rld/Lx5MzoCwPCpPjfK+n8Cg==",
+      "version": "0.6.4",
+      "resolved": "https://registry.npmjs.org/@babel/helper-define-polyfill-provider/-/helper-define-polyfill-provider-0.6.4.tgz",
+      "integrity": "sha512-jljfR1rGnXXNWnmQg2K3+bvhkxB51Rl32QRaOTuwwjviGrHzIbSc8+x9CpraDtbT7mfyjXObULP4w/adunNwAw==",
       "dev": true,
       "dependencies": {
         "@babel/helper-compilation-targets": "^7.22.6",
@@ -644,12 +643,12 @@
       }
     },
     "node_modules/@babel/plugin-transform-block-scoping": {
-      "version": "7.25.9",
-      "resolved": "https://registry.npmjs.org/@babel/plugin-transform-block-scoping/-/plugin-transform-block-scoping-7.25.9.tgz",
-      "integrity": "sha512-1F05O7AYjymAtqbsFETboN1NvBdcnzMerO+zlMyJBEz6WkMdejvGWw9p05iTSjC85RLlBseHHQpYaM4gzJkBGg==",
+      "version": "7.27.0",
+      "resolved": "https://registry.npmjs.org/@babel/plugin-transform-block-scoping/-/plugin-transform-block-scoping-7.27.0.tgz",
+      "integrity": "sha512-u1jGphZ8uDI2Pj/HJj6YQ6XQLZCNjOlprjxB5SVz6rq2T6SwAR+CdrWK0CP7F+9rDVMXdB0+r6Am5G5aobOjAQ==",
       "dev": true,
       "dependencies": {
-        "@babel/helper-plugin-utils": "^7.25.9"
+        "@babel/helper-plugin-utils": "^7.26.5"
       },
       "engines": {
         "node": ">=6.9.0"
@@ -834,12 +833,12 @@
       }
     },
     "node_modules/@babel/plugin-transform-for-of": {
-      "version": "7.25.9",
-      "resolved": "https://registry.npmjs.org/@babel/plugin-transform-for-of/-/plugin-transform-for-of-7.25.9.tgz",
-      "integrity": "sha512-LqHxduHoaGELJl2uhImHwRQudhCM50pT46rIBNvtT/Oql3nqiS3wOwP+5ten7NpYSXrrVLgtZU3DZmPtWZo16A==",
+      "version": "7.26.9",
+      "resolved": "https://registry.npmjs.org/@babel/plugin-transform-for-of/-/plugin-transform-for-of-7.26.9.tgz",
+      "integrity": "sha512-Hry8AusVm8LW5BVFgiyUReuoGzPUpdHQQqJY5bZnbbf+ngOHWuCuYFKw/BqaaWlvEUrF91HMhDtEaI1hZzNbLg==",
       "dev": true,
       "dependencies": {
-        "@babel/helper-plugin-utils": "^7.25.9",
+        "@babel/helper-plugin-utils": "^7.26.5",
         "@babel/helper-skip-transparent-expression-wrappers": "^7.25.9"
       },
       "engines": {
@@ -1246,12 +1245,12 @@
       }
     },
     "node_modules/@babel/plugin-transform-regenerator": {
-      "version": "7.25.9",
-      "resolved": "https://registry.npmjs.org/@babel/plugin-transform-regenerator/-/plugin-transform-regenerator-7.25.9.tgz",
-      "integrity": "sha512-vwDcDNsgMPDGP0nMqzahDWE5/MLcX8sv96+wfX7as7LoF/kr97Bo/7fI00lXY4wUXYfVmwIIyG80fGZ1uvt2qg==",
+      "version": "7.27.0",
+      "resolved": "https://registry.npmjs.org/@babel/plugin-transform-regenerator/-/plugin-transform-regenerator-7.27.0.tgz",
+      "integrity": "sha512-LX/vCajUJQDqE7Aum/ELUMZAY19+cDpghxrnyt5I1tV6X5PyC86AOoWXWFYFeIvauyeSA6/ktn4tQVn/3ZifsA==",
       "dev": true,
       "dependencies": {
-        "@babel/helper-plugin-utils": "^7.25.9",
+        "@babel/helper-plugin-utils": "^7.26.5",
         "regenerator-transform": "^0.15.2"
       },
       "engines": {
@@ -1354,9 +1353,9 @@
       }
     },
     "node_modules/@babel/plugin-transform-typeof-symbol": {
-      "version": "7.26.7",
-      "resolved": "https://registry.npmjs.org/@babel/plugin-transform-typeof-symbol/-/plugin-transform-typeof-symbol-7.26.7.tgz",
-      "integrity": "sha512-jfoTXXZTgGg36BmhqT3cAYK5qkmqvJpvNrPhaK/52Vgjhw4Rq29s9UqpWWV0D6yuRmgiFH/BUVlkl96zJWqnaw==",
+      "version": "7.27.0",
+      "resolved": "https://registry.npmjs.org/@babel/plugin-transform-typeof-symbol/-/plugin-transform-typeof-symbol-7.27.0.tgz",
+      "integrity": "sha512-+LLkxA9rKJpNoGsbLnAgOCdESl73vwYn+V6b+5wHbrE7OGKVDPHIQvbFSzqE6rwqaCw2RE+zdJrlLkcf8YOA0w==",
       "dev": true,
       "dependencies": {
         "@babel/helper-plugin-utils": "^7.26.5"
@@ -1369,13 +1368,13 @@
       }
     },
     "node_modules/@babel/plugin-transform-typescript": {
-      "version": "7.26.8",
-      "resolved": "https://registry.npmjs.org/@babel/plugin-transform-typescript/-/plugin-transform-typescript-7.26.8.tgz",
-      "integrity": "sha512-bME5J9AC8ChwA7aEPJ6zym3w7aObZULHhbNLU0bKUhKsAkylkzUdq+0kdymh9rzi8nlNFl2bmldFBCKNJBUpuw==",
+      "version": "7.27.0",
+      "resolved": "https://registry.npmjs.org/@babel/plugin-transform-typescript/-/plugin-transform-typescript-7.27.0.tgz",
+      "integrity": "sha512-fRGGjO2UEGPjvEcyAZXRXAS8AfdaQoq7HnxAbJoAoW10B9xOKesmmndJv+Sym2a+9FHWZ9KbyyLCe9s0Sn5jtg==",
       "dev": true,
       "dependencies": {
         "@babel/helper-annotate-as-pure": "^7.25.9",
-        "@babel/helper-create-class-features-plugin": "^7.25.9",
+        "@babel/helper-create-class-features-plugin": "^7.27.0",
         "@babel/helper-plugin-utils": "^7.26.5",
         "@babel/helper-skip-transparent-expression-wrappers": "^7.25.9",
         "@babel/plugin-syntax-typescript": "^7.25.9"
@@ -1451,9 +1450,9 @@
       }
     },
     "node_modules/@babel/preset-env": {
-      "version": "7.26.8",
-      "resolved": "https://registry.npmjs.org/@babel/preset-env/-/preset-env-7.26.8.tgz",
-      "integrity": "sha512-um7Sy+2THd697S4zJEfv/U5MHGJzkN2xhtsR3T/SWRbVSic62nbISh51VVfU9JiO/L/Z97QczHTaFVkOU8IzNg==",
+      "version": "7.26.9",
+      "resolved": "https://registry.npmjs.org/@babel/preset-env/-/preset-env-7.26.9.tgz",
+      "integrity": "sha512-vX3qPGE8sEKEAZCWk05k3cpTAE3/nOYca++JA+Rd0z2NCNzabmYvEiSShKzm10zdquOIAVXsy2Ei/DTW34KlKQ==",
       "dev": true,
       "dependencies": {
         "@babel/compat-data": "^7.26.8",
@@ -1485,7 +1484,7 @@
         "@babel/plugin-transform-dynamic-import": "^7.25.9",
         "@babel/plugin-transform-exponentiation-operator": "^7.26.3",
         "@babel/plugin-transform-export-namespace-from": "^7.25.9",
-        "@babel/plugin-transform-for-of": "^7.25.9",
+        "@babel/plugin-transform-for-of": "^7.26.9",
         "@babel/plugin-transform-function-name": "^7.25.9",
         "@babel/plugin-transform-json-strings": "^7.25.9",
         "@babel/plugin-transform-literals": "^7.25.9",
@@ -1548,9 +1547,9 @@
       }
     },
     "node_modules/@babel/preset-react": {
-      "version": "7.25.9",
-      "resolved": "https://registry.npmjs.org/@babel/preset-react/-/preset-react-7.25.9.tgz",
-      "integrity": "sha512-D3to0uSPiWE7rBrdIICCd0tJSIGpLaaGptna2+w7Pft5xMqLpA1sz99DK5TZ1TjGbdQ/VI1eCSZ06dv3lT4JOw==",
+      "version": "7.26.3",
+      "resolved": "https://registry.npmjs.org/@babel/preset-react/-/preset-react-7.26.3.tgz",
+      "integrity": "sha512-Nl03d6T9ky516DGK2YMxrTqvnpUW63TnJMOMonj+Zae0JiPC5BC9xPMSL6L8fiSpA5vP88qfygavVQvnLp+6Cw==",
       "dev": true,
       "dependencies": {
         "@babel/helper-plugin-utils": "^7.25.9",
@@ -1568,16 +1567,16 @@
       }
     },
     "node_modules/@babel/preset-typescript": {
-      "version": "7.26.0",
-      "resolved": "https://registry.npmjs.org/@babel/preset-typescript/-/preset-typescript-7.26.0.tgz",
-      "integrity": "sha512-NMk1IGZ5I/oHhoXEElcm+xUnL/szL6xflkFZmoEU9xj1qSJXpiS7rsspYo92B4DRCDvZn2erT5LdsCeXAKNCkg==",
+      "version": "7.27.0",
+      "resolved": "https://registry.npmjs.org/@babel/preset-typescript/-/preset-typescript-7.27.0.tgz",
+      "integrity": "sha512-vxaPFfJtHhgeOVXRKuHpHPAOgymmy8V8I65T1q53R7GCZlefKeCaTyDs3zOPHTTbmquvNlQYC5klEvWsBAtrBQ==",
       "dev": true,
       "dependencies": {
-        "@babel/helper-plugin-utils": "^7.25.9",
+        "@babel/helper-plugin-utils": "^7.26.5",
         "@babel/helper-validator-option": "^7.25.9",
         "@babel/plugin-syntax-jsx": "^7.25.9",
-        "@babel/plugin-transform-modules-commonjs": "^7.25.9",
-        "@babel/plugin-transform-typescript": "^7.25.9"
+        "@babel/plugin-transform-modules-commonjs": "^7.26.3",
+        "@babel/plugin-transform-typescript": "^7.27.0"
       },
       "engines": {
         "node": ">=6.9.0"
@@ -1611,15 +1610,15 @@
       }
     },
     "node_modules/@babel/traverse": {
-      "version": "7.26.8",
-      "resolved": "https://registry.npmjs.org/@babel/traverse/-/traverse-7.26.8.tgz",
-      "integrity": "sha512-nic9tRkjYH0oB2dzr/JoGIm+4Q6SuYeLEiIiZDwBscRMYFJ+tMAz98fuel9ZnbXViA2I0HVSSRRK8DW5fjXStA==",
+      "version": "7.27.0",
+      "resolved": "https://registry.npmjs.org/@babel/traverse/-/traverse-7.27.0.tgz",
+      "integrity": "sha512-19lYZFzYVQkkHkl4Cy4WrAVcqBkgvV2YM2TU3xG6DIwO7O3ecbDPfW3yM3bjAGcqcQHi+CCtjMR3dIEHxsd6bA==",
       "dependencies": {
         "@babel/code-frame": "^7.26.2",
-        "@babel/generator": "^7.26.8",
-        "@babel/parser": "^7.26.8",
-        "@babel/template": "^7.26.8",
-        "@babel/types": "^7.26.8",
+        "@babel/generator": "^7.27.0",
+        "@babel/parser": "^7.27.0",
+        "@babel/template": "^7.27.0",
+        "@babel/types": "^7.27.0",
         "debug": "^4.3.1",
         "globals": "^11.1.0"
       },
@@ -2192,28 +2191,21 @@
       }
     },
     "node_modules/@hello-pangea/dnd": {
-      "version": "17.0.0",
-      "resolved": "https://registry.npmjs.org/@hello-pangea/dnd/-/dnd-17.0.0.tgz",
-      "integrity": "sha512-LDDPOix/5N0j5QZxubiW9T0M0+1PR0rTDWeZF5pu1Tz91UQnuVK4qQ/EjY83Qm2QeX0eM8qDXANfDh3VVqtR4Q==",
+      "version": "18.0.1",
+      "resolved": "https://registry.npmjs.org/@hello-pangea/dnd/-/dnd-18.0.1.tgz",
+      "integrity": "sha512-xojVWG8s/TGrKT1fC8K2tIWeejJYTAeJuj36zM//yEm/ZrnZUSFGS15BpO+jGZT1ybWvyXmeDJwPYb4dhWlbZQ==",
       "dependencies": {
-        "@babel/runtime": "^7.25.6",
+        "@babel/runtime": "^7.26.7",
         "css-box-model": "^1.2.1",
-        "memoize-one": "^6.0.0",
         "raf-schd": "^4.0.3",
-        "react-redux": "^9.1.2",
-        "redux": "^5.0.1",
-        "use-memo-one": "^1.1.3"
+        "react-redux": "^9.2.0",
+        "redux": "^5.0.1"
       },
       "peerDependencies": {
-        "react": "^18.0.0",
-        "react-dom": "^18.0.0"
+        "react": "^18.0.0 || ^19.0.0",
+        "react-dom": "^18.0.0 || ^19.0.0"
       }
     },
-    "node_modules/@hello-pangea/dnd/node_modules/memoize-one": {
-      "version": "6.0.0",
-      "resolved": "https://registry.npmjs.org/memoize-one/-/memoize-one-6.0.0.tgz",
-      "integrity": "sha512-rkpe71W0N0c0Xz6QD0eJETuWAJGnJ9afsl1srmwPrI+yBCkge5EycXXbYRyvL29zZVUWQCY7InPRCv3GDXuZNw=="
-    },
     "node_modules/@icons/material": {
       "version": "0.2.4",
       "resolved": "https://registry.npmjs.org/@icons/material/-/material-0.2.4.tgz",
@@ -3046,8 +3038,9 @@
     },
     "node_modules/@jsonjoy.com/base64": {
       "version": "1.1.2",
+      "resolved": "https://registry.npmjs.org/@jsonjoy.com/base64/-/base64-1.1.2.tgz",
+      "integrity": "sha512-q6XAnWQDIMA3+FTiOYajoYqySkO+JSat0ytXGSuRdq9uXE7o92gzuQwQM14xaCRlBLGq3v5miDGC4vkVTn54xA==",
       "dev": true,
-      "license": "Apache-2.0",
       "engines": {
         "node": ">=10.0"
       },
@@ -3060,9 +3053,10 @@
       }
     },
     "node_modules/@jsonjoy.com/json-pack": {
-      "version": "1.1.0",
+      "version": "1.2.0",
+      "resolved": "https://registry.npmjs.org/@jsonjoy.com/json-pack/-/json-pack-1.2.0.tgz",
+      "integrity": "sha512-io1zEbbYcElht3tdlqEOFxZ0dMTYrHz9iMf0gqn1pPjZFTCgM5R4R5IMA20Chb2UPYYsxjzs8CgZ7Nb5n2K2rA==",
       "dev": true,
-      "license": "Apache-2.0",
       "dependencies": {
         "@jsonjoy.com/base64": "^1.1.1",
         "@jsonjoy.com/util": "^1.1.2",
@@ -3081,9 +3075,10 @@
       }
     },
     "node_modules/@jsonjoy.com/util": {
-      "version": "1.3.0",
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         "webpack-sources": "^3.2.3"
       },
@@ -11991,41 +12048,39 @@
       }
     },
     "node_modules/webpack-cli": {
-      "version": "5.1.4",
+      "version": "6.0.1",
+      "resolved": "https://registry.npmjs.org/webpack-cli/-/webpack-cli-6.0.1.tgz",
+      "integrity": "sha512-MfwFQ6SfwinsUVi0rNJm7rHZ31GyTcpVE5pgVA3hwFRb7COD4TzjUUwhGWKfO50+xdc2MQPuEBBJoqIMGt3JDw==",
       "dev": true,
-      "license": "MIT",
       "dependencies": {
-        "@discoveryjs/json-ext": "^0.5.0",
-        "@webpack-cli/configtest": "^2.1.1",
-        "@webpack-cli/info": "^2.0.2",
-        "@webpack-cli/serve": "^2.0.5",
+        "@discoveryjs/json-ext": "^0.6.1",
+        "@webpack-cli/configtest": "^3.0.1",
+        "@webpack-cli/info": "^3.0.1",
+        "@webpack-cli/serve": "^3.0.1",
         "colorette": "^2.0.14",
-        "commander": "^10.0.1",
+        "commander": "^12.1.0",
         "cross-spawn": "^7.0.3",
-        "envinfo": "^7.7.3",
+        "envinfo": "^7.14.0",
         "fastest-levenshtein": "^1.0.12",
         "import-local": "^3.0.2",
         "interpret": "^3.1.1",
         "rechoir": "^0.8.0",
-        "webpack-merge": "^5.7.3"
+        "webpack-merge": "^6.0.1"
       },
       "bin": {
         "webpack-cli": "bin/cli.js"
       },
       "engines": {
-        "node": ">=14.15.0"
+        "node": ">=18.12.0"
       },
       "funding": {
         "type": "opencollective",
         "url": "https://opencollective.com/webpack"
       },
       "peerDependencies": {
-        "webpack": "5.x.x"
+        "webpack": "^5.82.0"
       },
       "peerDependenciesMeta": {
-        "@webpack-cli/generators": {
-          "optional": true
-        },
         "webpack-bundle-analyzer": {
           "optional": true
         },
@@ -12034,18 +12089,29 @@
         }
       }
     },
+    "node_modules/webpack-cli/node_modules/@discoveryjs/json-ext": {
+      "version": "0.6.3",
+      "resolved": "https://registry.npmjs.org/@discoveryjs/json-ext/-/json-ext-0.6.3.tgz",
+      "integrity": "sha512-4B4OijXeVNOPZlYA2oEwWOTkzyltLao+xbotHQeqN++Rv27Y6s818+n2Qkp8q+Fxhn0t/5lA5X1Mxktud8eayQ==",
+      "dev": true,
+      "engines": {
+        "node": ">=14.17.0"
+      }
+    },
     "node_modules/webpack-cli/node_modules/commander": {
-      "version": "10.0.1",
+      "version": "12.1.0",
+      "resolved": "https://registry.npmjs.org/commander/-/commander-12.1.0.tgz",
+      "integrity": "sha512-Vw8qHK3bZM9y/P10u3Vib8o/DdkvA2OtPtZvD871QKjy74Wj1WSKFILMPRPSdUSx5RFK1arlJzEtA4PkFgnbuA==",
       "dev": true,
-      "license": "MIT",
       "engines": {
-        "node": ">=14"
+        "node": ">=18"
       }
     },
     "node_modules/webpack-dev-middleware": {
       "version": "7.4.2",
+      "resolved": "https://registry.npmjs.org/webpack-dev-middleware/-/webpack-dev-middleware-7.4.2.tgz",
+      "integrity": "sha512-xOO8n6eggxnwYpy1NlzUKpvrjfJTvae5/D6WOK0S2LSo7vjmo5gCM1DbLUmFqrMTJP+W/0YZNctm7jasWvLuBA==",
       "dev": true,
-      "license": "MIT",
       "dependencies": {
         "colorette": "^2.0.10",
         "memfs": "^4.6.0",
@@ -12071,9 +12137,10 @@
       }
     },
     "node_modules/webpack-dev-middleware/node_modules/memfs": {
-      "version": "4.11.1",
+      "version": "4.17.0",
+      "resolved": "https://registry.npmjs.org/memfs/-/memfs-4.17.0.tgz",
+      "integrity": "sha512-4eirfZ7thblFmqFjywlTmuWVSvccHAJbn1r8qQLzmTO11qcqpohOjmY2mFce6x7x7WtskzRqApPD0hv+Oa74jg==",
       "dev": true,
-      "license": "Apache-2.0",
       "dependencies": {
         "@jsonjoy.com/json-pack": "^1.0.3",
         "@jsonjoy.com/util": "^1.3.0",
@@ -12089,14 +12156,15 @@
       }
     },
     "node_modules/webpack-dev-server": {
-      "version": "5.1.0",
-      "resolved": "https://registry.npmjs.org/webpack-dev-server/-/webpack-dev-server-5.1.0.tgz",
-      "integrity": "sha512-aQpaN81X6tXie1FoOB7xlMfCsN19pSvRAeYUHOdFWOlhpQ/LlbfTqYwwmEDFV0h8GGuqmCmKmT+pxcUV/Nt2gQ==",
+      "version": "5.2.1",
+      "resolved": "https://registry.npmjs.org/webpack-dev-server/-/webpack-dev-server-5.2.1.tgz",
+      "integrity": "sha512-ml/0HIj9NLpVKOMq+SuBPLHcmbG+TGIjXRHsYfZwocUBIqEvws8NnS/V9AFQ5FKP+tgn5adwVwRrTEpGL33QFQ==",
       "dev": true,
       "dependencies": {
         "@types/bonjour": "^3.5.13",
         "@types/connect-history-api-fallback": "^1.5.4",
         "@types/express": "^4.17.21",
+        "@types/express-serve-static-core": "^4.17.21",
         "@types/serve-index": "^1.9.4",
         "@types/serve-static": "^1.15.5",
         "@types/sockjs": "^0.3.36",
@@ -12107,10 +12175,9 @@
         "colorette": "^2.0.10",
         "compression": "^1.7.4",
         "connect-history-api-fallback": "^2.0.0",
-        "express": "^4.19.2",
+        "express": "^4.21.2",
         "graceful-fs": "^4.2.6",
-        "html-entities": "^2.4.0",
-        "http-proxy-middleware": "^2.0.3",
+        "http-proxy-middleware": "^2.0.7",
         "ipaddr.js": "^2.1.0",
         "launch-editor": "^2.6.1",
         "open": "^10.0.3",
@@ -12145,71 +12212,80 @@
         }
       }
     },
-    "node_modules/webpack-merge": {
-      "version": "5.10.0",
+    "node_modules/webpack-dev-server/node_modules/chokidar": {
+      "version": "3.6.0",
+      "resolved": "https://registry.npmjs.org/chokidar/-/chokidar-3.6.0.tgz",
+      "integrity": "sha512-7VT13fmjotKpGipCW9JEQAusEPE+Ei8nl6/g4FBAmIm0GOOLMua9NDDo/DWp0ZAxCr3cPq5ZpBqmPAQgDda2Pw==",
       "dev": true,
-      "license": "MIT",
       "dependencies": {
-        "clone-deep": "^4.0.1",
-        "flat": "^5.0.2",
-        "wildcard": "^2.0.0"
+        "anymatch": "~3.1.2",
+        "braces": "~3.0.2",
+        "glob-parent": "~5.1.2",
+        "is-binary-path": "~2.1.0",
+        "is-glob": "~4.0.1",
+        "normalize-path": "~3.0.0",
+        "readdirp": "~3.6.0"
       },
       "engines": {
-        "node": ">=10.0.0"
+        "node": ">= 8.10.0"
+      },
+      "funding": {
+        "url": "https://paulmillr.com/funding/"
+      },
+      "optionalDependencies": {
+        "fsevents": "~2.3.2"
       }
     },
-    "node_modules/webpack-sources": {
-      "version": "3.2.3",
-      "license": "MIT",
+    "node_modules/webpack-dev-server/node_modules/glob-parent": {
+      "version": "5.1.2",
+      "resolved": "https://registry.npmjs.org/glob-parent/-/glob-parent-5.1.2.tgz",
+      "integrity": "sha512-AOIgSQCepiJYwP3ARnGx+5VnTu2HBYdzbGP45eLw1vr3zB3vZLeyed1sC9hnbcOc9/SrMyM5RPQrkGz4aS9Zow==",
+      "dev": true,
+      "dependencies": {
+        "is-glob": "^4.0.1"
+      },
       "engines": {
-        "node": ">=10.13.0"
+        "node": ">= 6"
       }
     },
-    "node_modules/webpack/node_modules/ajv": {
-      "version": "6.12.6",
-      "license": "MIT",
+    "node_modules/webpack-dev-server/node_modules/readdirp": {
+      "version": "3.6.0",
+      "resolved": "https://registry.npmjs.org/readdirp/-/readdirp-3.6.0.tgz",
+      "integrity": "sha512-hOS089on8RduqdbhvQ5Z37A0ESjsqz6qnRcffsMU3495FuTdqSm+7bhJ29JvIOsBDEEnan5DPu9t3To9VRlMzA==",
+      "dev": true,
       "dependencies": {
-        "fast-deep-equal": "^3.1.1",
-        "fast-json-stable-stringify": "^2.0.0",
-        "json-schema-traverse": "^0.4.1",
-        "uri-js": "^4.2.2"
+        "picomatch": "^2.2.1"
       },
-      "funding": {
-        "type": "github",
-        "url": "https://github.com/sponsors/epoberezkin"
+      "engines": {
+        "node": ">=8.10.0"
       }
     },
-    "node_modules/webpack/node_modules/ajv-keywords": {
-      "version": "3.5.2",
-      "license": "MIT",
-      "peerDependencies": {
-        "ajv": "^6.9.1"
+    "node_modules/webpack-merge": {
+      "version": "6.0.1",
+      "resolved": "https://registry.npmjs.org/webpack-merge/-/webpack-merge-6.0.1.tgz",
+      "integrity": "sha512-hXXvrjtx2PLYx4qruKl+kyRSLc52V+cCvMxRjmKwoA+CBbbF5GfIBtR6kCvl0fYGqTUPKB+1ktVmTHqMOzgCBg==",
+      "dev": true,
+      "dependencies": {
+        "clone-deep": "^4.0.1",
+        "flat": "^5.0.2",
+        "wildcard": "^2.0.1"
+      },
+      "engines": {
+        "node": ">=18.0.0"
       }
     },
-    "node_modules/webpack/node_modules/json-schema-traverse": {
-      "version": "0.4.1",
-      "license": "MIT"
-    },
-    "node_modules/webpack/node_modules/schema-utils": {
-      "version": "3.3.0",
+    "node_modules/webpack-sources": {
+      "version": "3.2.3",
       "license": "MIT",
-      "dependencies": {
-        "@types/json-schema": "^7.0.8",
-        "ajv": "^6.12.5",
-        "ajv-keywords": "^3.5.2"
-      },
       "engines": {
-        "node": ">= 10.13.0"
-      },
-      "funding": {
-        "type": "opencollective",
-        "url": "https://opencollective.com/webpack"
+        "node": ">=10.13.0"
       }
     },
     "node_modules/websocket-driver": {
       "version": "0.7.4",
+      "resolved": "https://registry.npmjs.org/websocket-driver/-/websocket-driver-0.7.4.tgz",
+      "integrity": "sha512-b17KeDIQVjvb0ssuSDF2cYXSg2iztliJ4B9WdsuB6J952qCPKmnVq4DyW5motImXHDC1cBT/1UezrJVsKw5zjg==",
       "dev": true,
-      "license": "Apache-2.0",
       "dependencies": {
         "http-parser-js": ">=0.5.1",
         "safe-buffer": ">=5.1.0",
@@ -12221,8 +12297,9 @@
     },
     "node_modules/websocket-extensions": {
       "version": "0.1.4",
+      "resolved": "https://registry.npmjs.org/websocket-extensions/-/websocket-extensions-0.1.4.tgz",
+      "integrity": "sha512-OqedPIGOfsDlo31UNwYbCFMSaO9m9G/0faIHj5/dZFDMFqPTcx6UwqyOy3COEaEOg/9VsGIpdqn62W5KhoKSpg==",
       "dev": true,
-      "license": "Apache-2.0",
       "engines": {
         "node": ">=0.8.0"
       }
@@ -12268,8 +12345,9 @@
     },
     "node_modules/wildcard": {
       "version": "2.0.1",
-      "dev": true,
-      "license": "MIT"
+      "resolved": "https://registry.npmjs.org/wildcard/-/wildcard-2.0.1.tgz",
+      "integrity": "sha512-CC1bOL87PIWSBhDcTrdeLo6eGT7mCFtrg0uIJtqJUFyK+eJnzl8A1niH56uu7KMa5XFrtiV+AQuHO3n7DsHnLQ==",
+      "dev": true
     },
     "node_modules/wrap-ansi": {
       "version": "7.0.0",
@@ -12308,9 +12386,10 @@
       "license": "ISC"
     },
     "node_modules/ws": {
-      "version": "8.18.0",
+      "version": "8.18.1",
+      "resolved": "https://registry.npmjs.org/ws/-/ws-8.18.1.tgz",
+      "integrity": "sha512-RKW2aJZMXeMxVpnZ6bck+RswznaxmzdULiBr6KY7XkTnW8uvt0iT9H5DkHUChXrc+uurzwa0rVI16n/Xzjdz1w==",
       "dev": true,
-      "license": "MIT",
       "engines": {
         "node": ">=10.0.0"
       },
@@ -12390,12 +12469,11 @@
       }
     },
     "node_modules/yocto-queue": {
-      "version": "1.1.1",
-      "resolved": "https://registry.npmjs.org/yocto-queue/-/yocto-queue-1.1.1.tgz",
-      "integrity": "sha512-b4JR1PFR10y1mKjhHY9LaGo6tmrgjit7hxVIeAmyMw3jegXR4dhYqLaQF5zMXZxY7tLpMyJeLjr1C4rLmkVe8g==",
-      "dev": true,
+      "version": "0.1.0",
+      "resolved": "https://registry.npmjs.org/yocto-queue/-/yocto-queue-0.1.0.tgz",
+      "integrity": "sha512-rVksvsnNCdJ/ohGc6xgPwyN8eheCxsiLM8mxuE/t/mOVqJewPuO1miLpTHQiRgTKCLexL4MeAFVagts7HmNZ2Q==",
       "engines": {
-        "node": ">=12.20"
+        "node": ">=10"
       },
       "funding": {
         "url": "https://github.com/sponsors/sindresorhus"
diff --git a/jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantWidget/ExtendedVariantWidget.tsx b/jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantWidget/ExtendedVariantWidget.tsx
index 1fe878691..107a19976 100644
--- a/jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantWidget/ExtendedVariantWidget.tsx
+++ b/jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantWidget/ExtendedVariantWidget.tsx
@@ -366,7 +366,7 @@ export default jbrowse => {
             return () => {
                 isApiSubscribed = false;
             };
-        }, [infoKeys])
+        }, [])
 
         let annTable;
         if (feat["INFO"]["ANN"]){
diff --git a/jbrowse/src/client/JBrowse/VariantSearch/components/FilterForm.tsx b/jbrowse/src/client/JBrowse/VariantSearch/components/FilterForm.tsx
index 1752cabcf..6a8346ea0 100644
--- a/jbrowse/src/client/JBrowse/VariantSearch/components/FilterForm.tsx
+++ b/jbrowse/src/client/JBrowse/VariantSearch/components/FilterForm.tsx
@@ -2,13 +2,15 @@ import React, { useState } from 'react';
 import TextField from '@mui/material/TextField';
 import Button from '@mui/material/Button';
 import Select from '@mui/material/Select';
+import ReactSelect from 'react-select';
 import AsyncSelect from 'react-select/async';
 import MenuItem from '@mui/material/MenuItem';
 import FormControl from '@mui/material/FormControl';
 import InputLabel from '@mui/material/InputLabel';
 import CardActions from '@mui/material/CardActions';
 import Card from '@mui/material/Card';
-import { FieldModel, Filter, getOperatorsForField, searchStringToInitialFilters } from '../../utils';
+import { FieldModel, Filter, searchStringToInitialFilters } from '../../utils';
+import { OperatorKey, OperatorRegistry } from '../operators';
 import KeyboardArrowDownIcon from '@mui/icons-material/KeyboardArrowDown';
 import { Box, Menu } from '@mui/material';
 import { styled } from '@mui/material/styles';
@@ -76,19 +78,22 @@ const SubmitAndExternal = styled('div')(({ theme }) => ({
 
 const FilterForm = (props: FilterFormProps ) => {
     const { handleQuery, setFilters, handleClose, fieldTypeInfo, allowedGroupNames, promotedFilters } = props
-    const [filters, localSetFilters] = useState<Filter[]>(searchStringToInitialFilters(fieldTypeInfo.map((x) => x.name)));
+    const initial = searchStringToInitialFilters(fieldTypeInfo.map(x => x.name))
+    const [filters, localSetFilters] = useState<Filter[]>(
+        initial.length ? initial : [ new Filter('', OperatorKey.None, '') ]
+    )
     const [highlightedInputs, setHighlightedInputs] = useState<{ [index: number]: { field: boolean, operator: boolean, value: boolean } }>({});
     const [commonFilterMenuOpen, setCommonFilterMenuOpen] = useState<boolean>(false)
     const buttonRef = React.useRef(null);
 
     const handleAddFilter = () => {
-        localSetFilters([...filters, new Filter()]);
+        localSetFilters([...filters, new Filter('', OperatorKey.None, '')]);
     };
 
     const handleRemoveFilter = (index) => {
         // If it's the last filter, just reset its values to default empty values
         if (filters.length === 1) {
-            localSetFilters([new Filter()]);
+            localSetFilters([new Filter('', OperatorKey.None, '')]);
         } else {
             // Otherwise, remove the filter normally
             localSetFilters(
@@ -99,64 +104,81 @@ const FilterForm = (props: FilterFormProps ) => {
         }
     };
 
-    const handleFilterChange = (index, key, value) => {
-        const newFilters = filters.map((filter, i) => {
-            if (i === index) {
-                const updatedFilter = Object.assign(new Filter(), { ...filter, [key]: value });
-
-                if (key === "operator") {
-                    if (value === "is empty" || value === "is not empty") {
-                        updatedFilter.value = '';
-                    }
-
-                    if (value === "in set" || filter.operator === "in set") {
-                        updatedFilter.value = ''; 
-                    }
-                }
+    const handleFilterChange = (
+      index: number,
+      key: 'field' | 'operator' | 'value',
+      value: any
+    ) => {
+      const newFilters = filters.map((filter, i) => {
+        if (i !== index) return filter;
+
+        const updatedFilter = Object.assign(
+          new Filter('', OperatorKey.None, ''),
+          { ...filter, [key]: value }
+        );
+
+        if (key === 'field') {
+          const fieldInfo = fieldTypeInfo.find(f => f.name === value);
+          const defaultOp = fieldInfo?.getDefaultOperator() ?? OperatorRegistry[OperatorKey.None];
+          updatedFilter.operator = defaultOp;
+          updatedFilter.value = '';
+        }
+        else if (key === 'operator') {
+          updatedFilter.operator = OperatorRegistry[value as OperatorKey];
+          updatedFilter.value = '';
+        }
 
-                return updatedFilter;
-            }
-            return filter;
-        });
+        return updatedFilter;
+      });
 
-        localSetFilters(newFilters);
+      localSetFilters(newFilters);
     };
 
+
     const handleSubmit = (event) => {
-        event.preventDefault();
-        const highlightedInputs = {};
-
-        filters.forEach((filter, index) => {
-            highlightedInputs[index] = { field: false, operator: false, value: false };
-
-            filter.field = filter.field ?? '';
-            filter.operator = filter.operator ?? '';
-            filter.value = filter.value ?? '';
-
-            if (filter.field === '') {
-                highlightedInputs[index].field = true;
-            }
-
-            if (filter.operator === '') {
-                highlightedInputs[index].operator = true;
-            }
-
-            if (filter.operator === 'is empty' || filter.operator === 'is not empty') {
-                filter.value = '';
-            } else if (filter.value === '') {
-                highlightedInputs[index].value = true;
-            }
-        });
-
-        const isSingleEmptyFilter = filters.length === 1 && !filters[0].field && !filters[0].operator && !filters[0].value;
-
-        setHighlightedInputs(highlightedInputs);
-        if (isSingleEmptyFilter || !Object.values(highlightedInputs).some(v => (v as any).field || (v as any).operator || (v as any).value)) {
-            handleQuery(filters);
-            setFilters(filters);
-            handleClose();
+      event.preventDefault()
+      const highlighted: Record<number, { field: boolean; operator: boolean; value: boolean }> = {}
+
+      filters.forEach((filter, i) => {
+        highlighted[i] = { field: false, operator: false, value: false }
+
+        filter.field = filter.field ?? ''
+        filter.value = filter.value ?? ''
+
+        if (!filter.field) {
+          highlighted[i].field = true
         }
-    };
+
+        if (!filter.operator.key) {
+          highlighted[i].operator = true
+        }
+
+        if (
+          filter.operator.key === OperatorKey.IsEmpty ||
+          filter.operator.key === OperatorKey.IsNotEmpty
+        ) {
+          filter.value = ''
+        } else if (!filter.value) {
+          highlighted[i].value = true
+        }
+      })
+
+      const isSingleEmpty =
+        filters.length === 1 &&
+        !filters[0].field &&
+        !filters[0].operator.key &&
+        !filters[0].value
+
+      setHighlightedInputs(highlighted)
+      if (
+        isSingleEmpty ||
+        !Object.values(highlighted).some(v => v.field || v.operator || v.value)
+      ) {
+        handleQuery(filters)
+        setFilters(filters)
+        handleClose?.()
+      }
+    }
 
     const handleMenuClose = () => {
         setCommonFilterMenuOpen(false)
@@ -211,55 +233,62 @@ const FilterForm = (props: FilterFormProps ) => {
                     <FormScroll>
                         {filters.map((filter, index) => (
                             <FilterRow key={index} >
-                                <FormControlMinWidth sx={ highlightedInputs[index]?.field ? highlightedSx : null }>
-                                  <InputLabel id="field-label">Field</InputLabel>
-                                  <Select
-                                        labelId="field-label"
-                                        label = 'Field'
-                                        value={filter.field}
-                                        onChange={(event) =>
-                                            handleFilterChange(index, "field", event.target.value)
+                                <FormControlMinWidth sx={highlightedInputs[index]?.field ? highlightedSx : null}>
+                                    <ReactSelect
+                                        inputId={`field-select-${index}`}
+                                        aria-labelledby={`field-label`}
+                                        placeholder="Select field..."
+                                        menuPortalTarget={document.body}
+                                        menuPosition="fixed"
+                                        styles={{
+                                            menuPortal: (base) => ({ ...base, zIndex: 9999 }),
+                                        }}
+                                        options={fieldTypeInfo.map(field => ({
+                                            value: field.name,
+                                            label: field.label ?? field.name,
+                                        }))}
+                                        onChange={(selected) =>
+                                            handleFilterChange(index, 'field', selected?.value ?? '')
                                         }
-                                    >
-                                        <MenuItem value="" style={{ display: 'none' }}>
-                                            <em>None</em>
-                                        </MenuItem>
-                                        {fieldTypeInfo.map((field) => (
-                                            <MenuItem key={field.name} value={field.name}>
-                                                {field.label ?? field.name}
-                                            </MenuItem>
-                                        ))}
-                                    </Select>
-                                </FormControlMinWidth>
-
-                                <FormControlMinWidth sx={ highlightedInputs[index]?.operator ? highlightedSx : null } >
-                                    <InputLabel id="operator-label">Operator</InputLabel>
-                                    <Select
-                                        labelId="operator-label"
-                                        label="Operator"
-                                        value={filter.operator}
-                                        onChange={(event) =>
-                                            handleFilterChange(index, "operator", event.target.value)
+                                        value={
+                                            filter.field
+                                                ? {
+                                                    value: filter.field,
+                                                    label: fieldTypeInfo.find(f => f.name === filter.field)?.label ?? filter.field
+                                                }
+                                                : null
                                         }
-                                    >
-                                        <MenuItem value="None" style={{ display: 'none' }}>
-                                            <em>None</em>
-                                        </MenuItem>
-
-                                        {getOperatorsForField(fieldTypeInfo.find(obj => obj.name === filter.field)) ? (
-                                            getOperatorsForField(fieldTypeInfo.find(obj => obj.name === filter.field)).map((operator) => (
-                                                <MenuItem key={operator} value={operator}>
-                                                    {operator}
-                                                </MenuItem>
-                                            ))
-                                        ) : (
-                                            <MenuItem></MenuItem>
-                                        )}
+                                        isClearable
+                                    />
+                                </FormControlMinWidth>
 
-                                    </Select>
+                                <FormControlMinWidth sx={highlightedInputs[index]?.operator ? highlightedSx : null}>
+                                  <InputLabel id="operator-label">Operator</InputLabel>
+                                  <Select
+                                    labelId="operator-label"
+                                    label="Operator"
+                                    value={filter.operator.key}
+                                    onChange={event =>
+                                      handleFilterChange(index, "operator", event.target.value as OperatorKey)
+                                    }
+                                  >
+                                    <MenuItem value={OperatorKey.None}>
+                                      <em>None</em>
+                                    </MenuItem>
+                                    {(() => {
+                                      const ops = fieldTypeInfo.find(f => f.name === filter.field)?.getOperators() ?? [];
+                                      return ops.length > 0
+                                        ? ops.map(op => (
+                                            <MenuItem key={op.key} value={op.key}>
+                                              {op.label}
+                                            </MenuItem>
+                                          ))
+                                        : <MenuItem />;
+                                    })()}
+                                  </Select>
                                 </FormControlMinWidth>
 
-                                {filter.operator === "in set" ? (
+                                {filter.operator.key === OperatorKey.EqualsOneOf ? (
                                     <FormControlMinWidth sx={ highlightedInputs[index]?.value ? highlightedSx : null } >
                                         <InputLabel id="value-select-label">Value</InputLabel>
                                         <Select
@@ -279,13 +308,14 @@ const FilterForm = (props: FilterFormProps ) => {
                                 ) : fieldTypeInfo.find(obj => obj.name === filter.field)?.allowableValues?.length > 1 ? (
                                     <FormControlMinWidth sx={ highlightedInputs[index]?.value ? highlightedSx : null } >
                                         <AsyncSelect
+                                            key={`async-${index}-${filter.operator.key}`}
                                             id={`value-select-${index}`}
                                             inputId={`value-select-${index}`}
                                             aria-labelledby={`value-select-${index}`}
                                             noOptionsMessage={() => 'Type to search...'}
                                             menuPortalTarget={document.body}
                                             menuPosition={'fixed'}
-                                            isDisabled={filter.operator === "is empty" || filter.operator === "is not empty"}
+                                            isDisabled={filter.operator.key === OperatorKey.IsEmpty || filter.operator.key === OperatorKey.IsNotEmpty}
                                             menuShouldBlockScroll={true}
                                             // See here: https://stackoverflow.com/questions/77625507/my-react-project-with-react-18-2-0-version-and-react-select-5-4-0-v
                                             styles={{ menuPortal: (base: any) => ({ ...base, zIndex: 9999 }) }}
@@ -300,8 +330,16 @@ const FilterForm = (props: FilterFormProps ) => {
                                                     .map(value => ({label: value, value}))
                                                 );
                                             }}
-                                            onChange={(selected) => handleFilterChange(index, "value", selected?.length > 0 ? selected.map(s => s.value).join(',') : undefined)}
-                                            value={filter.value ? filter.value.split(',').map(value => ({label: value, value})) : undefined}
+                                            onChange={(selected) => {
+                                                const arr = Array.isArray(selected) ? selected : [selected].filter(Boolean)
+                                                const val = arr.map(s => s.value).join(',')
+                                                handleFilterChange(index, 'value', val)
+                                            }}
+                                            value={
+                                                filter.value
+                                                  ? (filter.value as string).split(',').map(v => ({ label: v, value: v }))
+                                                  : null
+                                              }
                                         />
                                     </FormControlMinWidth>
                                 ) : fieldTypeInfo.find(obj => obj.name === filter.field)?.allowableValues?.length > 0 ? (
@@ -312,7 +350,7 @@ const FilterForm = (props: FilterFormProps ) => {
                                             label="Value"
                                             id={`value-select-${index}`}
                                             value={filter.value}
-                                            disabled={filter.operator === "is empty" || filter.operator === "is not empty"}
+                                            disabled={filter.operator.key === OperatorKey.IsEmpty || filter.operator.key === OperatorKey.IsNotEmpty}
                                             onChange={(event) =>
                                                 handleFilterChange(index, "value", event.target.value)
                                             }
@@ -331,7 +369,7 @@ const FilterForm = (props: FilterFormProps ) => {
                                         sx={ highlightedInputs[index]?.value ? highlightedSx : null }
                                         variant="outlined"
                                         value={filter.value}
-                                        disabled={filter.operator === "is empty" || filter.operator === "is not empty"}
+                                        disabled={filter.operator.key === OperatorKey.IsEmpty || filter.operator.key === OperatorKey.IsNotEmpty}
                                         onChange={(event) =>
                                             handleFilterChange(index, 'value', event.target.value)
                                         }
diff --git a/jbrowse/src/client/JBrowse/VariantSearch/components/ShareButton.tsx b/jbrowse/src/client/JBrowse/VariantSearch/components/ShareButton.tsx
new file mode 100644
index 000000000..2315158be
--- /dev/null
+++ b/jbrowse/src/client/JBrowse/VariantSearch/components/ShareButton.tsx
@@ -0,0 +1,25 @@
+import React from 'react';
+import { Button } from '@mui/material';
+import LinkIcon from '@mui/icons-material/Link';
+
+export const ShareButton = () => {
+  return (
+      <Button
+            startIcon={<LinkIcon />}
+            size="small"
+            color="primary"
+            onClick={() => {
+                navigator.clipboard.writeText(window.location.href)
+                .then(() => {
+                    alert('URL copied to clipboard.');
+                })
+                .catch(err => {
+                    console.error('Failed to copy the URL: ', err);
+                    alert('Failed to copy the URL.');
+                });
+            }}
+        >
+        Share
+      </Button>
+  );
+};
diff --git a/jbrowse/src/client/JBrowse/VariantSearch/components/VariantTableWidget.tsx b/jbrowse/src/client/JBrowse/VariantSearch/components/VariantTableWidget.tsx
index 9a186e493..8b5b799b4 100644
--- a/jbrowse/src/client/JBrowse/VariantSearch/components/VariantTableWidget.tsx
+++ b/jbrowse/src/client/JBrowse/VariantSearch/components/VariantTableWidget.tsx
@@ -13,7 +13,10 @@ import {
     GridToolbarExport
 } from '@mui/x-data-grid';
 import SearchIcon from '@mui/icons-material/Search';
+import { OperatorKey } from '../operators'
 import LinkIcon from '@mui/icons-material/Link';
+import DownloadIcon from '@mui/icons-material/Download'
+import { ActionURL } from '@labkey/api';
 import React, { useEffect, useState } from 'react';
 import { getConf } from '@jbrowse/core/configuration';
 import { AppBar, Box, Button, Dialog, Paper, Popover, Toolbar, Tooltip, Typography } from '@mui/material';
@@ -23,6 +26,7 @@ import { NoAssemblyRegion } from '@jbrowse/core/util/types';
 import { toArray } from 'rxjs/operators';
 import {
     createEncodedFilterString,
+    buildLuceneQuery,
     fetchFieldTypeInfo,
     fetchLuceneQuery,
     FieldModel,
@@ -37,8 +41,10 @@ import '../../jbrowse.css';
 import LoadingIndicator from './LoadingIndicator';
 import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { lastValueFrom } from 'rxjs';
+import { ShareButton } from  './ShareButton';
 
 const VariantTableWidget = observer(props => {
+    const numberFormatter = new Intl.NumberFormat('en-US');
     const { assembly, trackId, parsedLocString, sessionId, session, pluginManager } = props;
     const { assemblyNames = [], assemblyManager } = session ?? {};
     const { view } = session ?? {};
@@ -74,7 +80,7 @@ const VariantTableWidget = observer(props => {
         const { page = pageSizeModel.page, pageSize = pageSizeModel.pageSize } = pageQueryModel;
         const { field = "genomicPosition", sort = false } = sortQueryModel[0] ?? {};
 
-        const encodedSearchString = createEncodedFilterString(passedFilters, false);
+        const encodedSearchString = createEncodedFilterString(passedFilters);
         const currentUrl = new URL(window.location.href);
         currentUrl.searchParams.set("searchString", encodedSearchString);
         currentUrl.searchParams.set("page", page.toString());
@@ -91,6 +97,27 @@ const VariantTableWidget = observer(props => {
         fetchLuceneQuery(passedFilters, sessionId, trackGUID, page, pageSize, field, sort, (json)=>{handleSearch(json)}, (error) => {setDataLoaded(true); setError(error)});
     }
 
+    const handleExport = () => {
+        const currentUrl = new URL(window.location.href);
+
+        const searchString = encodeURIComponent(buildLuceneQuery(filters));
+        const sortField = sortModel[0]?.field ?? 'genomicPosition';
+        const sortDirection = sortModel[0]?.sort ?? false;
+
+        const sortReverse = (sortDirection === 'desc');
+
+        const rawUrl = ActionURL.buildURL('jbrowse', 'luceneCSVExport.api');
+        const exportUrl = new URL(rawUrl, window.location.origin);
+
+        exportUrl.searchParams.set('sessionId', sessionId);
+        exportUrl.searchParams.set('trackId', trackGUID);
+        exportUrl.searchParams.set('searchString', searchString);
+        exportUrl.searchParams.set('sortField', sortField);
+        exportUrl.searchParams.set('sortReverse', sortReverse.toString());
+
+        window.location.href = exportUrl.toString();
+    };
+
     const TableCellWithPopover = (props: { value: any }) => {
         const { value } = props;
         const fullDisplayValue = value ? (Array.isArray(value) ? value.join(', ') : value) : ''
@@ -183,7 +210,7 @@ const VariantTableWidget = observer(props => {
         );
     }
 
-    function CustomToolbar({ setFilterModalOpen }) {
+    function CustomToolbar({ setFilterModalOpen, handleExport }) {
         return (
             <GridToolbarContainer>
                 <GridToolbarColumnsButton />
@@ -196,35 +223,25 @@ const VariantTableWidget = observer(props => {
                     Search
                 </Button>
                 <GridToolbarDensitySelector />
-                <GridToolbarExport csvOptions={{
-                    delimiter: ';',
-                }} />
 
                 <Button
-                    startIcon={<LinkIcon />}
-                    size="small"
+                    startIcon={<DownloadIcon />}
                     color="primary"
-                    onClick={() => {
-                        navigator.clipboard.writeText(window.location.href)
-                        .then(() => {
-                            // Popup message for successful copy
-                            alert('URL copied to clipboard.');
-                        })
-                        .catch(err => {
-                            // Error handling
-                            console.error('Failed to copy the URL: ', err);
-                            alert('Failed to copy the URL.');
-                        });
-                    }}
+                    onClick={handleExport}
                 >
-                Share
+                    Export CSV
                 </Button>
+
+                <ShareButton />
             </GridToolbarContainer>
         );
     }
 
     const ToolbarWithProps = () => (
-        <CustomToolbar setFilterModalOpen={setFilterModalOpen} />
+        <CustomToolbar
+            setFilterModalOpen={setFilterModalOpen}
+            handleExport={handleExport}
+        />
     );
 
     const handleOffsetChange = (newOffset: number) => {
@@ -469,6 +486,14 @@ const VariantTableWidget = observer(props => {
                 setSortModel(newModel)
                 handleQuery(filters, true, { page: 0, pageSize: pageSizeModel.pageSize }, newModel);
             }}
+            localeText={{
+                MuiTablePagination: {
+                    labelDisplayedRows: ({ from, to, count }) =>
+                        `${numberFormatter.format(from)}–${numberFormatter.format(to)} of ${
+                            count !== -1 ? numberFormatter.format(count) : 'more than ' + numberFormatter.format(to)
+                        }`,
+                    },
+                }}
         />
     )
 
@@ -529,14 +554,14 @@ const VariantTableWidget = observer(props => {
             <div style={{ marginBottom: "10px", display: "flex", alignItems: "center" }}>
                 <div style={{ flex: 1 }}>
                     {filters.map((filter, index) => {
-                        if ((filter as any).field && ((filter as any).operator === "is empty" || (filter as any).operator === "is not empty") && !(filter as any).value) {
+                        if ((filter as any).field && ((filter as any).operator.key === OperatorKey.IsEmpty || (filter as any).operator.key === OperatorKey.IsNotEmpty) && !(filter as any).value) {
                             return (
                                 <Button
                                     key={index}
                                     onClick={() => setFilterModalOpen(true)}
                                     style={{ border: "1px solid gray", margin: "5px" }}
                                 >
-                                    {`${(filter as any).field} ${(filter as any).operator}`}
+                                    {`${(filter as any).field} ${(filter as any).operator.key}`}
                                 </Button>
                             );
                         }
@@ -554,7 +579,7 @@ const VariantTableWidget = observer(props => {
                                 key={index}
                                 onClick={() => setFilterModalOpen(true)}
                                 style={{ border: "1px solid gray", margin: "5px" }}                            >
-                                {`${(filter as any).field} ${(filter as any).operator} ${(filter as any).value}`}
+                                {`${(filter as any).field} ${(filter as any).operator.key} ${(filter as any).value}`}
                             </Button>
                         );
                     })}
diff --git a/jbrowse/src/client/JBrowse/VariantSearch/operators.ts b/jbrowse/src/client/JBrowse/VariantSearch/operators.ts
new file mode 100644
index 000000000..928f502de
--- /dev/null
+++ b/jbrowse/src/client/JBrowse/VariantSearch/operators.ts
@@ -0,0 +1,185 @@
+export enum OperatorKey {
+  Equals             = 'equals',
+  NotEquals          = 'does not equal',
+  Contains           = 'contains',
+  NotContains        = 'does not contain',
+  StartsWith         = 'starts with',
+  EndsWith           = 'ends with',
+  IsEmpty            = 'is empty',
+  IsNotEmpty         = 'is not empty',
+  NumericEq          = '=',
+  NumericNeq         = '!=',
+  NumericGt          = '>',
+  NumericGte         = '>=',
+  NumericLt          = '<',
+  NumericLte         = '<=',
+  IsIn             = 'is in',
+  IsNotIn          = 'is not in',
+  IsInAllOf        = 'is in all of',
+  IsInAnyOf        = 'is in any of',
+  IsNotInAnyOf     = 'is not in any of',
+  IsNotInOneOf     = 'is not in one of',
+  EqualsOneOf        = 'equals one of',
+  None              = ''
+}
+
+export type Value = string | number
+
+export interface Operator<T extends Value = Value> {
+  key: OperatorKey
+  label: string
+  generateLucene(field: string, value: T): string
+}
+
+function fuzzyNumRange(field: string, raw: string | number) {
+  const floatValue = parseFloat(String(raw))
+  const intValue   = parseInt(String(raw), 10)
+
+  if (floatValue === intValue) {
+    return `[${intValue} TO ${intValue}]`
+  }
+
+  return `[${floatValue - 0.000001} TO ${floatValue + 0.000001}]`
+}
+
+function fuzzyGtRange(f: string, raw: string | number) {
+  const floatValue = parseFloat(String(raw))
+  const intValue   = parseInt(String(raw), 10)
+  if (floatValue !== intValue) {
+    return `${f}:[${floatValue + 0.000001} TO *]`
+  }
+  return `${f}:{${intValue} TO *]`
+}
+
+function fuzzyLtRange(f: string, raw: string | number) {
+  const floatValue = parseFloat(String(raw))
+  const intValue   = parseInt(String(raw), 10)
+  if (floatValue !== intValue) {
+    return `${f}:[* TO ${floatValue - 0.000001}]`
+  }
+  return `${f}:[* TO ${intValue}}`
+}
+
+export const OperatorRegistry: Record<OperatorKey, Operator> = {
+  [OperatorKey.Equals]: {
+    key: OperatorKey.Equals,
+    label: 'Equals',
+    generateLucene: (f, v: string) => `${f}:${v}`,
+  },
+  [OperatorKey.NotEquals]: {
+    key: OperatorKey.NotEquals,
+    label: 'Does Not Equal',
+    generateLucene: (f, v: string) => `*:* -${f}:${v}`,
+  },
+  [OperatorKey.Contains]: {
+    key: OperatorKey.Contains,
+    label: 'Contains',
+    generateLucene: (f, v: string) => `${f}:*${v}*`,
+  },
+  [OperatorKey.NotContains]: {
+    key: OperatorKey.NotContains,
+    label: 'Does Not Contain',
+    generateLucene: (f, v: string) => `*:* -${f}:*${v}*`,
+  },
+  [OperatorKey.StartsWith]: {
+    key: OperatorKey.StartsWith,
+    label: 'Starts With',
+    generateLucene: (f, v: string) => `${f}:${v}*`,
+  },
+  [OperatorKey.EndsWith]: {
+    key: OperatorKey.EndsWith,
+    label: 'Ends With',
+    generateLucene: (f, v: string) => `${f}:*${v}`,
+  },
+  [OperatorKey.IsEmpty]: {
+    key: OperatorKey.IsEmpty,
+    label: 'Is Empty',
+    generateLucene: (f) => `*:* -${f}:*`,
+  },
+  [OperatorKey.IsNotEmpty]: {
+    key: OperatorKey.IsNotEmpty,
+    label: 'Is Not Empty',
+    generateLucene: (f) => `${f}:*`,
+  },
+  [OperatorKey.NumericEq]: {
+    key: OperatorKey.NumericEq,
+    label: '=',
+    generateLucene: (f, v: number) =>
+      Number.isInteger(v) ? `${f}:[${v} TO ${v}]` : `${f}:${fuzzyNumRange(f, v)}`,
+  },
+  [OperatorKey.NumericNeq]: {
+    key: OperatorKey.NumericNeq,
+    label: '!=',
+    generateLucene: (f, v: number) => {
+      if (Number.isInteger(v)) {
+        return `*:* -${f}:[${v} TO ${v}]`
+      }
+      const range = fuzzyNumRange(f, v)
+      return `*:* -${f}:${range}`
+    },
+  },
+  [OperatorKey.NumericGt]: {
+    key: OperatorKey.NumericGt,
+    label: '>',
+    generateLucene: fuzzyGtRange,
+  },
+  [OperatorKey.NumericGte]: {
+    key: OperatorKey.NumericGte,
+    label: '>=',
+    generateLucene: (f, v: number) => `${f}:[${v} TO *]`,
+  },
+  [OperatorKey.NumericLt]: {
+    key: OperatorKey.NumericLt,
+    label: '<',
+    generateLucene: fuzzyLtRange,
+  },
+  [OperatorKey.NumericLte]: {
+    key: OperatorKey.NumericLte,
+    label: '<=',
+    generateLucene: (f, v: number) => `${f}:[* TO ${v}]`,
+  },
+  [OperatorKey.EqualsOneOf]: {
+    key: OperatorKey.EqualsOneOf,
+    label: 'Equals One Of',
+    generateLucene: (f, v: string) => `${f}:~${v}~`,
+  },
+ [OperatorKey.IsIn]: {
+    key: OperatorKey.IsIn,
+    label: 'Is In',
+    generateLucene: (f, v: string) => `${f}:${v}`,
+  },
+  [OperatorKey.IsNotIn]: {
+    key: OperatorKey.IsNotIn,
+    label: 'Is Not In',
+    generateLucene: (f, v: string) => `*:* -${f}:${v}`,
+  },
+  [OperatorKey.IsInAllOf]: {
+    key: OperatorKey.IsInAllOf,
+    label: 'Is In All Of',
+    generateLucene: (f, v: string) =>
+      v.split(',').map(val => `+${f}:${val}`).join(' '),
+  },
+  [OperatorKey.IsInAnyOf]: {
+    key: OperatorKey.IsInAnyOf,
+    label: 'Is In Any Of',
+    generateLucene: (f, v: string) =>
+      v.split(',').map(val => `${f}:${val}`).join(' OR '),
+  },
+  [OperatorKey.IsNotInAnyOf]: {
+    key: OperatorKey.IsNotInAnyOf,
+    label: 'Is Not In Any Of',
+    generateLucene: (f, v: string) =>
+      v.split(',').map(val => `*:* -${f}:${val}`).join(' AND '),
+  },
+  [OperatorKey.IsNotInOneOf]: {
+    key: OperatorKey.IsNotInOneOf,
+    label: 'Is Not In One Of',
+    generateLucene: (f, v: string) =>
+      v.split(',').map(val => `*:* -${f}:${val}`).join(' OR '),
+  },
+  [OperatorKey.None]: {
+    key: OperatorKey.None,
+    label: '',
+    generateLucene: () => ''
+  }
+}
\ No newline at end of file
diff --git a/jbrowse/src/client/JBrowse/VariantTable/components/ShareButton.tsx b/jbrowse/src/client/JBrowse/VariantTable/components/ShareButton.tsx
new file mode 100644
index 000000000..2315158be
--- /dev/null
+++ b/jbrowse/src/client/JBrowse/VariantTable/components/ShareButton.tsx
@@ -0,0 +1,25 @@
+import React from 'react';
+import { Button } from '@mui/material';
+import LinkIcon from '@mui/icons-material/Link';
+
+export const ShareButton = () => {
+  return (
+      <Button
+            startIcon={<LinkIcon />}
+            size="small"
+            color="primary"
+            onClick={() => {
+                navigator.clipboard.writeText(window.location.href)
+                .then(() => {
+                    alert('URL copied to clipboard.');
+                })
+                .catch(err => {
+                    console.error('Failed to copy the URL: ', err);
+                    alert('Failed to copy the URL.');
+                });
+            }}
+        >
+        Share
+      </Button>
+  );
+};
diff --git a/jbrowse/src/client/JBrowse/VariantTable/components/VariantTableWidget.tsx b/jbrowse/src/client/JBrowse/VariantTable/components/VariantTableWidget.tsx
index a7b58ebc4..33f61a49d 100644
--- a/jbrowse/src/client/JBrowse/VariantTable/components/VariantTableWidget.tsx
+++ b/jbrowse/src/client/JBrowse/VariantTable/components/VariantTableWidget.tsx
@@ -3,7 +3,17 @@ import React, { useEffect, useState } from 'react';
 import { getConf } from '@jbrowse/core/configuration';
 import { ParsedLocString, parseLocString } from '@jbrowse/core/util';
 import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache';
-import { AppBar, Box, Button, Dialog, Grid, MenuItem, Paper, Toolbar, Typography } from '@mui/material';
+import {
+    AppBar,
+    Box,
+    Button,
+    Dialog,
+    Grid,
+    MenuItem,
+    Paper,
+    Toolbar,
+    Typography,
+} from '@mui/material';
 import ScopedCssBaseline from '@mui/material/ScopedCssBaseline';
 import {
   DataGrid,
@@ -11,7 +21,11 @@ import {
   GridColumnVisibilityModel, GridFilterPanel,
   GridPaginationModel,
   GridRenderCellParams,
-  GridToolbar
+  GridToolbar,
+  GridToolbarColumnsButton,
+  GridToolbarFilterButton,
+  GridToolbarDensitySelector,
+  GridToolbarExport
 } from '@mui/x-data-grid';
 import MenuButton from './MenuButton';
 import '../../jbrowse.css';
@@ -27,6 +41,7 @@ import {
   passesSampleFilters
 } from '../../utils';
 import LoadingIndicator from './LoadingIndicator';
+import { ShareButton } from './ShareButton';
 import { NoAssemblyRegion } from '@jbrowse/core/util/types';
 import StandaloneSearchComponent from '../../Search/components/StandaloneSearchComponent';
 import { VcfFeature } from '@jbrowse/plugin-variants';
@@ -352,12 +367,24 @@ const VariantTableWidget = observer(props => {
     }
   }
 
+  const CustomToolbar = () => (
+    <Box sx={{ display: 'flex', justifyContent: 'space-between', p: 1 }}>
+      <Box>
+        <GridToolbarColumnsButton />
+        <GridToolbarFilterButton />
+        <GridToolbarDensitySelector />
+        <GridToolbarExport />
+        <ShareButton />
+      </Box>
+    </Box>
+  );
+
   const gridElement = (
     // NOTE: the filterPanel/sx override is added to fix an issue where the grid column filter value input doesn't align with the field and operator inputs
     <DataGrid
         columns={[...gridColumns, actionsCol]}
         rows={features.map((rawFeature, id) => rawFeatureToRow(rawFeature, id, gridColumns, trackId))}
-        slots={{ toolbar: GridToolbar, filterPanel: GridFilterPanel }}
+        slots={{ toolbar: CustomToolbar, filterPanel: GridFilterPanel }}
         slotProps={{
           filterPanel: {
             filterFormProps: {
@@ -444,7 +471,7 @@ const VariantTableWidget = observer(props => {
           </Grid>
 
           {supportsLuceneIndex ? <Grid key='luceneViewButton' item xs="auto">
-            <Button hidden={!supportsLuceneIndex} style={{ marginTop:"8px"}} color="primary" variant="contained" onClick={() => handleMenu("luceneRedirect")}>Switch to Free-text Search</Button>
+            <Button hidden={!supportsLuceneIndex} style={{ marginTop:"8px"}} color="primary" variant="contained" onClick={() => handleMenu("luceneRedirect")}>Switch to Full-text Search</Button>
           </Grid> : null}
         </Grid>
       </div>
diff --git a/jbrowse/src/client/JBrowse/utils.ts b/jbrowse/src/client/JBrowse/utils.ts
index 1602ff088..75fa6a195 100644
--- a/jbrowse/src/client/JBrowse/utils.ts
+++ b/jbrowse/src/client/JBrowse/utils.ts
@@ -12,6 +12,7 @@ import {
 } from '@mui/x-data-grid';
 import { ParsedLocString, parseLocString } from '@jbrowse/core/util';
 import { VcfFeature } from '@jbrowse/plugin-variants';
+import { Operator, OperatorKey, OperatorRegistry, Value } from './VariantSearch/operators'
 
 export function arrayMax(array) {
     return Array.isArray(array) ? Math.max(...array) : array
@@ -239,7 +240,7 @@ export function navigateToSearch(sessionId, locString, trackId, isValidRefNameFo
         const start = parsedLocString.start;
         const end = parsedLocString.end;
 
-        searchString = serializeLocationToLuceneQuery(contig, start, end)
+        searchString = serializeLocationToEncodedSearchString(contig, start, end)
     }
 
     window.location.href = ActionURL.buildURL("jbrowse", "variantSearch.view", null, {session: sessionId, location: locString, trackId: trackId, activeTracks: trackId, sampleFilters: sampleFilterURL, infoFilters: infoFilterURL, searchString: searchString})
@@ -317,106 +318,14 @@ export function getGenotypeURL(trackId, contig, start, end) {
     return ActionURL.buildURL("jbrowse", "genotypeTable.view", null, {trackId: trackId, chr: contig, start: start, stop: end})
 }
 
-export function serializeLocationToLuceneQuery(contig, start, end) {
+export function serializeLocationToEncodedSearchString(contig, start, end) {
     const filters = [
-        {field: "contig", operator: "equals", value: contig.toString()},
-        {field: "start", operator: ">=", value: start.toString()},
-        {field: "end", operator: "<=", value: end.toString()}
+        new Filter("contig", OperatorKey.Equals, contig.toString()),
+        new Filter("start", OperatorKey.NumericGte, start.toString()),
+        new Filter("end", OperatorKey.NumericLte, end.toString())
     ]
 
-    return createEncodedFilterString(filters, false)
-}
-
-function generateLuceneString(field, operator, value) {
-  let luceneQueryString = '';
-
-  if (field === 'variableSamples' && operator == "in set") {
-    return `variableSamples:~${value}~`;
-  }
-  let intValue = parseInt(value);
-  let floatValue = parseFloat(value);
-
-  // Generate Lucene query string based on operator and type of value
-  switch (operator) {
-    case '=': // Exact match for numeric fields
-        luceneQueryString = floatValue !== intValue 
-            ? `${field}:[${Number(value) - 0.000001} TO ${Number(value) + 0.000001}]`
-            : `${field}:[${value} TO ${value}]`;
-        break;
-    case '!=': // Not equal to, for numeric fields
-        luceneQueryString = floatValue !== intValue 
-            ? `${field}:[* TO ${Number(value) - 0.000001}] OR ${field}:[${Number(value) + 0.000001} TO *]` 
-            : `${field}:[* TO ${value}} OR ${field}:{${value} TO *]`;
-        break;
-    case '>': // Greater than for numeric fields
-        luceneQueryString = floatValue !== intValue 
-            ? `${field}:[${Number(value) + 0.000001} TO *]`
-            : `${field}:{${value} TO *]`;
-        break;
-    case '>=': // Greater than or equal to for numeric fields
-        luceneQueryString = `${field}:[${value} TO *]`;
-        break;
-    case '<': // Less than for numeric fields
-        luceneQueryString = floatValue !== intValue 
-            ? `${field}:[* TO ${Number(value) - 0.000001}]`
-            : `${field}:[* TO ${value}}`;
-        break;
-    case '<=': // Less than or equal to for numeric fields
-        luceneQueryString = `${field}:[* TO ${value}]`;
-        break;
-    case 'equals': // Exact match for string fields
-        luceneQueryString = `${field}:${value}`;
-        break;
-    case 'contains': // Substring search for string fields
-        luceneQueryString = `${field}:*${value}*`;
-        break;
-    case 'does not equal': // Not equal to for string fields
-        luceneQueryString = `*:* -${field}:${value}`;
-        break;
-    case 'does not contain': // Does not contain for string fields
-        luceneQueryString = `*:* -${field}:*${value}*`;
-        break;
-    case 'starts with': // Starts with for string fields
-        luceneQueryString = `${field}:${value}*`;
-        break;
-    case 'ends with': // Ends with for string fields
-        luceneQueryString = `${field}:*${value}`;
-        break;
-    case 'is empty': // Field is empty
-        luceneQueryString = `*:* -${field}:*`;
-        break;
-    case 'is not empty': // Field is not empty
-        luceneQueryString = `${field}:*`;
-        break;
-    case 'variable in': // Variable in for multi-valued fields
-        luceneQueryString = `${field}:${value}`;
-        break;
-    case 'not variable in': // Not variable in for multi-valued fields
-        luceneQueryString = `*:* -${field}:${value}`;
-        break;
-    default:
-        // Operators that require multiple values
-        const values = value.split(',');
-
-        switch (operator) {
-        case 'variable in all of': // Variable in all of the provided values
-            luceneQueryString = values.map(v => `+${field}:${v}`).join(' ');
-            break;
-        case 'variable in any of': // Variable in any of the provided values
-            luceneQueryString = values.map(v => `${field}:${v}`).join(' OR ');
-            break;
-        case 'not variable in any of': // Not variable in any of the provided values
-            luceneQueryString = values.map(v => `*:* -${field}:${v}`).join(' AND ');
-            break;
-        case 'not variable in one of': // Not variable in one of the provided values
-            luceneQueryString = values.map(v => `*:* -${field}:${v}`).join(' OR ');
-            break;
-        default:
-            throw new Error(`Invalid operator: ${operator}`);
-        }
-    }
-
-  return luceneQueryString;
+    return createEncodedFilterString(filters)
 }
 
 export async function fetchLuceneQuery(filters, sessionId, trackGUID, offset, pageSize, sortField, sortReverseString, successCallback, failureCallback) {
@@ -439,6 +348,9 @@ export async function fetchLuceneQuery(filters, sessionId, trackGUID, offset, pa
         return
     }
 
+    const lucene = buildLuceneQuery(filters)
+    const encoded = encodeURIComponent(lucene)
+
     let sortReverse;
     if(sortReverseString == "asc") {
         sortReverse = true
@@ -457,7 +369,7 @@ export async function fetchLuceneQuery(filters, sessionId, trackGUID, offset, pa
             failureCallback("There was an error: " + res.status + "\n Status Body: " + res.responseText + "\n Session ID:" + sessionId)
         },
         params: {
-            "searchString": createEncodedFilterString(filters, true),
+            "searchString": encoded,
             "sessionId": sessionId,
             "trackId": trackGUID,
             "offset": offset,
@@ -468,23 +380,6 @@ export async function fetchLuceneQuery(filters, sessionId, trackGUID, offset, pa
     });
 }
 
-export function createEncodedFilterString(filters: Array<{field: string; operator: string; value: string}>, lucenify: boolean) {
-    let ret: any = []
-
-    if(!filters || filters.length == 0 || (filters.length == 1 && filters[0].field == "" && filters[0].operator == "" && filters[0].value == "")) {
-        return "all"
-    }
-
-    if(lucenify) {
-        ret = filters.map(val => generateLuceneString(val.field, val.operator, val.value));
-    } else {
-        ret = filters.map(val => val.field + "," + val.operator + "," + val.value)
-    }
-    const concatenatedString = ret.join('&');
-
-    return encodeURIComponent(concatenatedString.replace(/\+/g, "%2B"));
-}
-
 export class FieldModel {
     name: string
     label: string
@@ -501,6 +396,7 @@ export class FieldModel {
     url: string
     flex: number
     supportsFilter: boolean = true
+    defaultOperator: string
 
     getLabel(): string {
         return this.label ?? this.name
@@ -525,6 +421,58 @@ export class FieldModel {
         return muiFieldType
     }
 
+    getOperators(): Operator[] {
+        if (this.name === 'variableSamples') {
+          return [
+            OperatorKey.EqualsOneOf,
+            OperatorKey.IsIn,
+            OperatorKey.IsNotIn,
+            OperatorKey.IsInAllOf,
+            OperatorKey.IsInAnyOf,
+            OperatorKey.IsNotInAnyOf,
+            OperatorKey.IsNotInOneOf,
+            OperatorKey.IsEmpty,
+            OperatorKey.IsNotEmpty,
+          ].map(k => OperatorRegistry[k])
+        }
+
+        switch (this.type) {
+          case 'String':
+          case 'Flag':
+          case 'Character':
+          case 'Impact':
+            return [
+              OperatorKey.Equals,
+              OperatorKey.NotEquals,
+              OperatorKey.Contains,
+              OperatorKey.NotContains,
+              OperatorKey.StartsWith,
+              OperatorKey.EndsWith,
+              OperatorKey.IsEmpty,
+              OperatorKey.IsNotEmpty,
+            ].map(k => OperatorRegistry[k])
+
+          case 'Float':
+          case 'Integer':
+            return [
+              OperatorKey.NumericEq,
+              OperatorKey.NumericNeq,
+              OperatorKey.NumericGt,
+              OperatorKey.NumericGte,
+              OperatorKey.NumericLt,
+              OperatorKey.NumericLte,
+            ].map(k => OperatorRegistry[k])
+
+          default:
+            return []
+        }
+    }
+
+    getDefaultOperator(): Operator | undefined {
+        if (this.defaultOperator && this.defaultOperator != "") return OperatorRegistry[this.defaultOperator]
+        return this.getOperators()[0]
+    }
+
     toGridColDef(): GridColDef {
         let gridCol: GridColDef = {
             field: this.name,
@@ -562,6 +510,19 @@ export class FieldModel {
     }
 }
 
+export function createEncodedFilterString(filters: Filter[]): string {
+    if (!filters.length || filters.every(f => f.isEmpty())) return 'all'
+    return encodeURIComponent(filters.map(f => f.encode()).join('&'))
+}
+
+export function buildLuceneQuery(filters: Filter[]): string {
+  if (!filters.length || filters.every(f => f.isEmpty())) return 'all'
+  return filters
+      .filter(f => !f.isEmpty())
+      .map(f => f.toLucene())
+      .join('&')
+}
+
 export async function fetchFieldTypeInfo(sessionId: string, trackId: string, successCallback: (fields: FieldModel[], groups: string[], promotedFilters: Map<string, Filter[]>) => void, failureCallback) {
     if (!sessionId || !trackId) {
         console.error("Cannot fetch field type info: sessionId or trackId not provided")
@@ -601,46 +562,45 @@ export function truncateToValidGUID(str: string) {
     return str;
 }
 
-export declare type FilterType = {
-    field: string,
-    value: any,
-    operator: string
-}
+export class Filter {
+  field: string
+  operator: Operator
+  value: Value
 
-export class Filter implements FilterType {
-    field: string = ""
-    value: any = ""
-    operator: string = ""
-
-    encode(): string {
-        return [this.field, this.operator, this.value].join(',')
-    }
+  constructor(field: string, operatorKey: OperatorKey, value: Value) {
+    this.field = field
+    this.operator = OperatorRegistry[operatorKey]
+    this.value = value
+  }
 
-    isEmpty(): boolean {
-        return !!this.field
-    }
+  encode(): string {
+    return [this.field, this.operator.key, this.value].join(',')
+  }
 
-    static fromString(str: string): Filter[] {
-        const decodedSearchString = decodeURIComponent(str)
-        const searchStringsArray = decodedSearchString.split("&").filter((x) => x !== "all")
+  toLucene(): string {
+    return this.operator.generateLucene(this.field, this.value as any)
+  }
 
-        return searchStringsArray.map((item) => {
-            const parts = item.split(",");
-            const field = parts[0];
-            const operator = parts[1];
-            const value = parts.slice(2).join(",");
-            return Object.assign(new Filter(), { field: field, operator: operator, value: value })
-        })
-    }
+  isEmpty(): boolean {
+    return this.field === ''
+  }
 
-    static deduplicate(filters: Filter[]): Filter[] {
-        const filterMap = {}
-        filters.forEach((f) => {
-            filterMap[f.encode()] = f
-        })
+  static fromString(str: string): Filter[] {
+    const decoded = decodeURIComponent(str)
+    return decoded
+      .split('&')
+      .filter(x => x !== 'all')
+      .map(item => {
+        const [field, opKey, ...valParts] = item.split(',')
+        const value = valParts.join(',')
+        return new Filter(field, opKey as OperatorKey, isNaN(Number(value)) ? value : Number(value))
+      })
+  }
 
-        return Object.keys(filterMap).map((key) => filterMap[key])
-    }
+  static deduplicate(filters: Filter[]): Filter[] {
+    const map = new Map(filters.map(f => [f.encode(), f]))
+    return Array.from(map.values())
+  }
 }
 
 export function searchStringToInitialFilters(knownFieldNames: string[]) : Filter[] {
@@ -651,49 +611,9 @@ export function searchStringToInitialFilters(knownFieldNames: string[]) : Filter
         return Filter.fromString(searchString).filter(({ field }) => knownFieldNames.includes(field))
     }
 
-    return [new Filter()]
+    return []
 }
 
-export function getOperatorsForField(fieldObj: FieldModel): string[] {
-    const stringOperators = ["equals", "does not equal", "contains", "does not contain", "starts with", "ends with", "is empty", "is not empty"];
-    const variableSamplesType = ["in set", "variable in", "not variable in", "variable in all of", "variable in any of", "not variable in any of", "not variable in one of", "is empty", "is not empty"];
-    const numericOperators = ["=", "!=", ">", ">=", "<", "<="];
-    const noneOperators = [];
-
-    // This can occur for the blank placeholder field:
-    if (!fieldObj) {
-        return[]
-    }
-
-    const field = fieldObj.name;
-    const type = fieldObj.type;
-
-    let allowedOperators;
-    switch (type) {
-        case 'Flag':
-        case 'String':
-        case 'Character':
-            allowedOperators = stringOperators;
-            break;
-        case 'Float':
-        case 'Integer':
-            allowedOperators = numericOperators;
-            break;
-        case 'Impact':
-            allowedOperators = stringOperators;
-            break;
-        case 'None':
-        default:
-            allowedOperators = noneOperators;
-            break;
-    }
-
-    if (field === "variableSamples") {
-        return variableSamplesType
-    }
-
-    return allowedOperators
-}
 
 export const multiValueComparator: GridComparatorFn = (v1, v2) => {
     return arrayMax(parseCellValue(v1)) - arrayMax(parseCellValue(v2))
diff --git a/jbrowse/src/org/labkey/jbrowse/JBrowseController.java b/jbrowse/src/org/labkey/jbrowse/JBrowseController.java
index caaf68229..6dc297b95 100644
--- a/jbrowse/src/org/labkey/jbrowse/JBrowseController.java
+++ b/jbrowse/src/org/labkey/jbrowse/JBrowseController.java
@@ -20,6 +20,7 @@
 import htsjdk.variant.variantcontext.Genotype;
 import htsjdk.variant.variantcontext.VariantContext;
 import htsjdk.variant.vcf.VCFFileReader;
+import jakarta.servlet.http.HttpServletResponse;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.logging.log4j.Logger;
 import org.jetbrains.annotations.NotNull;
@@ -78,6 +79,8 @@
 import java.io.File;
 import java.io.FileNotFoundException;
 import java.io.IOException;
+import java.time.LocalDateTime;
+import java.time.format.DateTimeFormatter;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collections;
@@ -891,6 +894,55 @@ public void validateForm(ResolveVcfFieldsForm form, Errors errors)
         }
     }
 
+    @RequiresPermission(ReadPermission.class)
+    public static class LuceneCSVExportAction extends ReadOnlyApiAction<LuceneQueryForm>
+    {
+        @Override
+        public ApiResponse execute(LuceneQueryForm form, BindException errors)
+        {
+            try
+            {
+                JBrowseLuceneSearch searcher = JBrowseLuceneSearch.create(form.getSessionId(), form.getTrackId(), getUser());
+                DateTimeFormatter formatter = DateTimeFormatter.ofPattern("yyyy-MM-dd_HH-mm-ss");
+                String timestamp = LocalDateTime.now().format(formatter);
+                String filename = "mGAP_results_" + timestamp + ".csv";
+
+                HttpServletResponse response = getViewContext().getResponse();
+                response.setContentType("text/csv");
+                response.setHeader("Content-Disposition", "attachment; filename=\"" + filename + "\"");
+
+                searcher.doSearchCSV(
+                        getUser(),
+                        PageFlowUtil.decode(form.getSearchString()),
+                        form.getSortField(),
+                        form.getSortReverse(),
+                        response
+                );
+
+                return null;
+            }
+            catch (Exception e)
+            {
+                _log.error("Error in JBrowse lucene query", e);
+                errors.reject(ERROR_MSG, e.getMessage());
+                return null;
+            }
+        }
+
+        @Override
+        public void validateForm(LuceneQueryForm form, Errors errors)
+        {
+            if ((form.getSearchString() == null || form.getSessionId() == null || form.getTrackId() == null))
+            {
+                errors.reject(ERROR_MSG, "Must provide search string, track ID, and the JBrowse session ID");
+            }
+            else if (!isValidUUID(form.getTrackId()))
+            {
+                errors.reject(ERROR_MSG, "Invalid track ID: " + form.getTrackId());
+            }
+        }
+    }
+
     @RequiresPermission(ReadPermission.class)
     public static class LuceneQueryAction extends ReadOnlyApiAction<LuceneQueryForm>
     {
@@ -910,7 +962,14 @@ public ApiResponse execute(LuceneQueryForm form, BindException errors)
 
             try
             {
-                return new ApiSimpleResponse(searcher.doSearch(getUser(), PageFlowUtil.decode(form.getSearchString()), form.getPageSize(), form.getOffset(), form.getSortField(), form.getSortReverse()));
+                return new ApiSimpleResponse(searcher.doSearchJSON(
+                        getUser(),
+                        PageFlowUtil.decode(form.getSearchString()),
+                        form.getPageSize(),
+                        form.getOffset(),
+                        form.getSortField(),
+                        form.getSortReverse()
+                ));
             }
             catch (Exception e)
             {
diff --git a/jbrowse/src/org/labkey/jbrowse/JBrowseLuceneSearch.java b/jbrowse/src/org/labkey/jbrowse/JBrowseLuceneSearch.java
index e0f57ea64..d4a58e168 100644
--- a/jbrowse/src/org/labkey/jbrowse/JBrowseLuceneSearch.java
+++ b/jbrowse/src/org/labkey/jbrowse/JBrowseLuceneSearch.java
@@ -1,5 +1,6 @@
 package org.labkey.jbrowse;
 
+import jakarta.servlet.http.HttpServletResponse;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.logging.log4j.Logger;
 import org.apache.lucene.analysis.Analyzer;
@@ -20,6 +21,7 @@
 import org.apache.lucene.search.MatchAllDocsQuery;
 import org.apache.lucene.search.Query;
 import org.apache.lucene.search.QueryCachingPolicy;
+import org.apache.lucene.search.ScoreDoc;
 import org.apache.lucene.search.Sort;
 import org.apache.lucene.search.SortField;
 import org.apache.lucene.search.TopFieldDocs;
@@ -49,6 +51,7 @@
 
 import java.io.File;
 import java.io.IOException;
+import java.io.PrintWriter;
 import java.net.URLDecoder;
 import java.nio.charset.StandardCharsets;
 import java.text.DecimalFormat;
@@ -189,7 +192,17 @@ public String extractFieldName(String queryString)
         return parts.length > 0 ? parts[0].trim() : null;
     }
 
-    public JSONObject doSearch(User u, String searchString, final int pageSize, final int offset, String sortField, boolean sortReverse) throws IOException, ParseException
+    public JSONObject doSearchJSON(User u, String searchString, final int pageSize, final int offset, String sortField, boolean sortReverse) throws IOException, ParseException {
+        SearchConfig searchConfig = createSearchConfig(u, searchString, pageSize, offset, sortField, sortReverse);
+        return paginateJSON(searchConfig);
+    }
+
+    public void doSearchCSV(User u, String searchString, String sortField, boolean sortReverse, HttpServletResponse response) throws IOException, ParseException {
+        SearchConfig searchConfig = createSearchConfig(u, searchString, 0, 0, sortField, sortReverse);
+        exportCSV(searchConfig, response);
+    }
+
+    private SearchConfig createSearchConfig(User u, String searchString, final int pageSize, final int offset, String sortField, boolean sortReverse) throws IOException, ParseException
     {
         searchString = tryUrlDecode(searchString);
         File indexPath = _jsonFile.getExpectedLocationOfLuceneIndex(true);
@@ -199,6 +212,7 @@ public JSONObject doSearch(User u, String searchString, final int pageSize, fina
         Analyzer analyzer = new StandardAnalyzer();
 
         List<String> stringQueryParserFields = new ArrayList<>();
+        List<String> fieldsList = new ArrayList<>();
         Map<String, SortField.Type> numericQueryParserFields = new HashMap<>();
         PointsConfig intPointsConfig = new PointsConfig(new DecimalFormat(), Integer.class);
         PointsConfig doublePointsConfig = new PointsConfig(new DecimalFormat(), Double.class);
@@ -208,6 +222,7 @@ public JSONObject doSearch(User u, String searchString, final int pageSize, fina
         for (Map.Entry<String, JBrowseFieldDescriptor> entry : fields.entrySet())
         {
             String field = entry.getKey();
+            fieldsList.add(field);
             JBrowseFieldDescriptor descriptor = entry.getValue();
 
             switch(descriptor.getType())
@@ -267,14 +282,14 @@ else if (numericQueryParserFields.containsKey(fieldName))
                 }
                 catch (QueryNodeException e)
                 {
-                    _log.error("Unable to parse query for field " + fieldName + ": " + queryString, e);
+                    _log.error("Unable to parse query for field {}: {}", fieldName, queryString, e);
 
                     throw new IllegalArgumentException("Unable to parse query: " + queryString + " for field: " + fieldName);
                 }
             }
             else
             {
-                _log.error("No such field(s), or malformed query: " + queryString + ", field: " + fieldName);
+                _log.error("No such field(s), or malformed query: {}, field: {}", queryString, fieldName);
 
                 throw new IllegalArgumentException("No such field(s), or malformed query: " + queryString + ", field: " + fieldName);
             }
@@ -302,43 +317,79 @@ else if (numericQueryParserFields.containsKey(fieldName))
             sort = new Sort(new SortField(sortField + "_sort", fieldType, sortReverse));
         }
 
+        return new SearchConfig(cacheEntry, query, pageSize, offset, sort, fieldsList);
+    }
+
+    private JSONObject paginateJSON(SearchConfig c) throws IOException, ParseException {
         // Get chunks of size {pageSize}. Default to 1 chunk -- add to the offset to get more.
         // We then iterate over the range of documents we want based on the offset. This does grow in memory
         // linearly with the number of documents, but my understanding is that these are just score,id pairs
         // rather than full documents, so mem usage *should* still be pretty low.
         // Perform the search with sorting
-        TopFieldDocs topDocs = cacheEntry.indexSearcher.search(query, pageSize * (offset + 1), sort);
-
+        TopFieldDocs topDocs = c.cacheEntry.indexSearcher.search(c.query, c.pageSize * (c.offset + 1), c.sort);
         JSONObject results = new JSONObject();
 
         // Iterate over the doc list, (either to the total end or until the page ends) grab the requested docs,
         // and add to returned results
         List<JSONObject> data = new ArrayList<>();
-        for (int i = pageSize * offset; i < Math.min(pageSize * (offset + 1), topDocs.scoreDocs.length); i++)
+        for (int i = c.pageSize * c.offset; i < Math.min(c.pageSize * (c.offset + 1), topDocs.scoreDocs.length); i++)
         {
             JSONObject elem = new JSONObject();
-            Document doc = cacheEntry.indexSearcher.storedFields().document(topDocs.scoreDocs[i].doc);
+            Document doc = c.cacheEntry.indexSearcher.storedFields().document(topDocs.scoreDocs[i].doc);
 
-            for (IndexableField field : doc.getFields()) {
+            for (IndexableField field : doc.getFields())
+            {
                 String fieldName = field.name();
                 String[] fieldValues = doc.getValues(fieldName);
-                if (fieldValues.length > 1) {
+                if (fieldValues.length > 1)
+                {
                     elem.put(fieldName, fieldValues);
-                } else {
+                }
+                else
+                {
                     elem.put(fieldName, fieldValues[0]);
                 }
             }
-
             data.add(elem);
         }
 
         results.put("data", data);
         results.put("totalHits", topDocs.totalHits.value);
 
-        //TODO: we should probably stream this
         return results;
     }
 
+    private void exportCSV(SearchConfig c, HttpServletResponse response) throws IOException
+    {
+        PrintWriter writer = response.getWriter();
+        IndexSearcher searcher = c.cacheEntry.indexSearcher;
+        TopFieldDocs topDocs = searcher.search(c.query, Integer.MAX_VALUE, c.sort);
+
+        writer.println(String.join(",", c.fields));
+
+        for (ScoreDoc scoreDoc : topDocs.scoreDocs)
+        {
+            Document doc = searcher.storedFields().document(scoreDoc.doc);
+            List<String> rowValues = new ArrayList<>();
+
+            for (String fieldName : c.fields)
+            {
+                String[] values = doc.getValues(fieldName);
+                String value = values.length > 0
+                        ? String.join(",", values)
+                        : "";
+
+                // Escape strings
+                value = "\"" + value.replace("\"", "\"\"") + "\"";
+                rowValues.add(value);
+            }
+
+            writer.println(String.join(",", rowValues));
+        }
+
+        writer.flush();
+    }
+
     public static class DefaultJBrowseFieldCustomizer extends AbstractJBrowseFieldCustomizer
     {
         public DefaultJBrowseFieldCustomizer()
@@ -583,7 +634,7 @@ public void cacheDefaultQuery()
         try
         {
             JBrowseLuceneSearch.clearCache(_jsonFile.getObjectId());
-            doSearch(_user, ALL_DOCS, 100, 0, GENOMIC_POSITION, false);
+            doSearchJSON(_user, ALL_DOCS, 100, 0, GENOMIC_POSITION, false);
         }
         catch (ParseException | IOException e)
         {
@@ -641,4 +692,22 @@ public void shutdownStarted()
             JBrowseLuceneSearch.emptyCache();
         }
     }
+
+    private class SearchConfig {
+        CacheEntry cacheEntry;
+        Query query;
+        int pageSize;
+        int offset;
+        Sort sort;
+        List<String> fields;
+
+        public SearchConfig(CacheEntry cacheEntry, Query query, int pageSize, int offset, Sort sort, List<String> fields) {
+            this.cacheEntry = cacheEntry;
+            this.query = query;
+            this.pageSize = pageSize;
+            this.offset = offset;
+            this.sort = sort;
+            this.fields = fields;
+        }
+    }
 }
diff --git a/jbrowse/test/src/org/labkey/test/tests/external/labModules/JBrowseTest.java b/jbrowse/test/src/org/labkey/test/tests/external/labModules/JBrowseTest.java
index 2199ccc99..9ee4094ac 100644
--- a/jbrowse/test/src/org/labkey/test/tests/external/labModules/JBrowseTest.java
+++ b/jbrowse/test/src/org/labkey/test/tests/external/labModules/JBrowseTest.java
@@ -15,6 +15,7 @@
  */
 package org.labkey.test.tests.external.labModules;
 
+import au.com.bytecode.opencsv.CSVReader;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.tuple.Pair;
 import org.json.JSONArray;
@@ -50,6 +51,7 @@
 import org.openqa.selenium.support.Color;
 
 import java.io.File;
+import java.io.FileReader;
 import java.io.IOException;
 import java.util.List;
 import java.util.Map;
@@ -569,7 +571,6 @@ private void testFullTextSearch() throws Exception
         String sessionId = info.getKey();
         String trackId = info.getValue();
 
-
         // all
         // this should return 143 results. We can't make any other assumptions about the content
         String url = "/jbrowse/" + getProjectName() + "/luceneQuery.view?sessionId=" + sessionId + "&trackId=" + trackId + "&searchString=all&pageSize=143";
@@ -1613,110 +1614,110 @@ private void testLuceneSearchUI(String sessionId)
 
         // VariableSamples in set !TestGroup!
         waitAndClick(Locator.tagWithText("button", "Search"));
-        waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "field-label")).click();
-        waitForElement(Locator.tagWithText("li", "Samples With Variant")).click();
+        waitForElement(Locator.tagWithAttribute("input", "aria-labelledby", "field-label")).click();
+        waitForElement(Locator.tagWithAttribute("div", "role", "listbox").child(Locator.tagWithText("div", "Samples With Variant"))).click();
         waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "operator-label")).click();
-        waitForElement(Locator.tagWithText("li", "in set")).click();
+        waitForElement(Locator.tagWithText("li", "Equals One Of")).click();
         waitForElement(Locator.tagWithId("div", "value-select-0")).click();
         waitForElement(Locator.tagWithText("li", "!TestGroup!")).click();
         waitAndClick(Locator.tagWithClass("button", "filter-form-select-button"));
         waitForElementToDisappear(Locator.tagWithText("span", "173"));
-        clearFilterDialog("variableSamples in set !TestGroup!");
+        clearFilterDialog("variableSamples equals one of !TestGroup!");
 
         // VariableSamples variable in m000001
         waitAndClick(Locator.tagWithText("button", "Search"));
-        waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "field-label")).click();
-        waitForElement(Locator.tagWithText("li", "Samples With Variant")).click();
+        waitForElement(Locator.tagWithAttribute("input", "aria-labelledby", "field-label")).click();
+        waitForElement(Locator.tagWithAttribute("div", "role", "listbox").child(Locator.tagWithText("div", "Samples With Variant"))).click();
         waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "operator-label")).click();
-        waitForElement(Locator.tagWithText("li", "variable in")).click();
+        waitForElement(Locator.tagWithText("li", "Is In")).click();
         waitForElement(Locator.tagWithId("input", "value-select-0")).sendKeys("m00001");
         waitForElement(Locator.tagWithId("input", "value-select-0")).sendKeys(Keys.ENTER);
         waitAndClick(Locator.tagWithClass("button", "filter-form-select-button"));
         waitForElement(Locator.tagWithText("span", "0.553"));
-        clearFilterDialog("variableSamples variable in m00001");
+        clearFilterDialog("variableSamples is in m00001");
 
         // VariableSamples not variable in m05710
         waitAndClick(Locator.tagWithText("button", "Search"));
-        waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "field-label")).click();
-        waitForElement(Locator.tagWithText("li", "Samples With Variant")).click();
+        waitForElement(Locator.tagWithAttribute("input", "aria-labelledby", "field-label")).click();
+        waitForElement(Locator.tagWithAttribute("div", "role", "listbox").child(Locator.tagWithText("div", "Samples With Variant"))).click();
         waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "operator-label")).click();
-        waitForElement(Locator.tagWithText("li", "not variable in")).click();
+        waitForElement(Locator.tagWithText("li", "Is Not In")).click();
         waitForElement(Locator.tagWithId("input", "value-select-0")).sendKeys("m05710");
         waitForElement(Locator.tagWithId("input", "value-select-0")).sendKeys(Keys.ENTER);
         waitAndClick(Locator.tagWithClass("button", "filter-form-select-button"));
         waitForElementToDisappear(Locator.tagWithText("span", "3.277E-4"));
-        clearFilterDialog("variableSamples not variable in m05710");
+        clearFilterDialog("variableSamples is not in m05710");
 
         // VariableSamples li usage + variable in all of
         waitAndClick(Locator.tagWithText("button", "Search"));
-        waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "field-label")).click();
-        waitForElement(Locator.tagWithText("li", "Samples With Variant")).click();
+        waitForElement(Locator.tagWithAttribute("input", "aria-labelledby", "field-label")).click();
+        waitForElement(Locator.tagWithAttribute("div", "role", "listbox").child(Locator.tagWithText("div", "Samples With Variant"))).click();
         waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "operator-label")).click();
-        waitForElement(Locator.tagWithText("li", "variable in all of")).click();
+        waitForElement(Locator.tagWithText("li", "Is In All Of")).click();
         waitForElement(Locator.tagWithId("input", "value-select-0")).sendKeys("m000");
         waitForElement(Locator.tagWithText("div", "m00005")).click();
         waitForElement(Locator.tagWithId("input", "value-select-0")).sendKeys("m000");
         waitForElement(Locator.tagWithText("div", "m00004")).click();
         waitAndClick(Locator.tagWithClass("button", "filter-form-select-button"));
         waitForElement(Locator.tagWithText("span", "0.3"));
-        clearFilterDialog("variableSamples variable in all of m00005,m00004");
+        clearFilterDialog("variableSamples is in all of m00005,m00004");
 
         // VariableSamples variable in any of m00004,m00007
         waitAndClick(Locator.tagWithText("button", "Search"));
-        waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "field-label")).click();
-        waitForElement(Locator.tagWithText("li", "Samples With Variant")).click();
+        waitForElement(Locator.tagWithAttribute("input", "aria-labelledby", "field-label")).click();
+        waitForElement(Locator.tagWithAttribute("div", "role", "listbox").child(Locator.tagWithText("div", "Samples With Variant"))).click();
         waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "operator-label")).click();
-        waitForElement(Locator.tagWithText("li", "variable in any of")).click();
+        waitForElement(Locator.tagWithText("li", "Is In Any Of")).click();
         waitForElement(Locator.tagWithId("input", "value-select-0")).sendKeys("m000");
         waitForElement(Locator.tagWithText("div", "m00004")).click();
         waitForElement(Locator.tagWithId("input", "value-select-0")).sendKeys("m000");
         waitForElement(Locator.tagWithText("div", "m00007")).click();
         waitAndClick(Locator.tagWithClass("button", "filter-form-select-button"));
         waitForElement(Locator.tagWithText("span", "2"));
-        clearFilterDialog("variableSamples variable in any of m00004,m00007");
+        clearFilterDialog("variableSamples is in any of m00004,m00007");
 
         // VariableSamples not variable in any of m00005,m00004
         waitAndClick(Locator.tagWithText("button", "Search"));
-        waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "field-label")).click();
-        waitForElement(Locator.tagWithText("li", "Samples With Variant")).click();
+        waitForElement(Locator.tagWithAttribute("input", "aria-labelledby", "field-label")).click();
+        waitForElement(Locator.tagWithAttribute("div", "role", "listbox").child(Locator.tagWithText("div", "Samples With Variant"))).click();
         waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "operator-label")).click();
-        waitForElement(Locator.tagWithText("li", "not variable in any of")).click();
+        waitForElement(Locator.tagWithText("li", "Is Not In Any Of")).click();
         waitForElement(Locator.tagWithId("input", "value-select-0")).sendKeys("m000");
         waitForElement(Locator.tagWithText("div", "m00005")).click();
         waitForElement(Locator.tagWithId("input", "value-select-0")).sendKeys("m000");
         waitForElement(Locator.tagWithText("div", "m00004")).click();
         waitAndClick(Locator.tagWithClass("button", "filter-form-select-button"));
         waitForElementToDisappear(Locator.tagWithText("span", "2"));
-        clearFilterDialog("variableSamples not variable in any of m00005,m00004");
+        clearFilterDialog("variableSamples is not in any of m00005,m00004");
 
         // VariableSamples not variable in one of m03660,m00001
         waitAndClick(Locator.tagWithText("button", "Search"));
-        waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "field-label")).click();
-        waitForElement(Locator.tagWithText("li", "Samples With Variant")).click();
+        waitForElement(Locator.tagWithAttribute("input", "aria-labelledby", "field-label")).click();
+        waitForElement(Locator.tagWithAttribute("div", "role", "listbox").child(Locator.tagWithText("div", "Samples With Variant"))).click();
         waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "operator-label")).click();
-        waitForElement(Locator.tagWithText("li", "not variable in one of")).click();
+        waitForElement(Locator.tagWithText("li", "Is Not In One Of")).click();
         waitForElement(Locator.tagWithId("input", "value-select-0")).sendKeys("m036");
         waitForElement(Locator.tagWithText("div", "m03660")).click();
         waitForElement(Locator.tagWithId("input", "value-select-0")).sendKeys("m000");
         waitForElement(Locator.tagWithText("div", "m00001")).click();
         waitAndClick(Locator.tagWithClass("button", "filter-form-select-button"));
         waitForElementToDisappear(Locator.tagWithText("span", "609"));
-        clearFilterDialog("variableSamples not variable in one of m03660,m00001");
+        clearFilterDialog("variableSamples is not in one of m03660,m00001");
 
         // samples with variant isEmpty
         waitAndClick(Locator.tagWithText("button", "Search"));
-        waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "field-label")).click();
-        waitForElement(Locator.tagWithText("li", "Samples With Variant")).click();
+        waitForElement(Locator.tagWithAttribute("input", "aria-labelledby", "field-label")).click();
+        waitForElement(Locator.tagWithAttribute("div", "role", "listbox").child(Locator.tagWithText("div", "Samples With Variant"))).click();
         waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "operator-label")).click();
-        waitForElement(Locator.tagWithText("li", "is empty")).click();
+        waitForElement(Locator.tagWithText("li", "Is Empty")).click();
         waitAndClick(Locator.tagWithClass("button", "filter-form-select-button"));
         waitForElementToDisappear(Locator.tagWithText("span", "2"));
         clearFilterDialog("variableSamples is empty");
 
         // Start = 2
         waitAndClick(Locator.tagWithText("button", "Search"));
-        waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "field-label")).click();
-        waitForElement(Locator.tagWithText("li", "Start")).click();
+        waitForElement(Locator.tagWithAttribute("input", "aria-labelledby", "field-label")).click();
+        waitForElement(Locator.tagWithAttribute("div", "role", "listbox").child(Locator.tagWithText("div", "Start"))).click();
         waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "operator-label")).click();
         waitForElement(Locator.tagWithText("li", "=")).click();
         waitForElement(Locator.tagWithId("input", "value-select-0")).sendKeys("2");
@@ -1726,8 +1727,8 @@ private void testLuceneSearchUI(String sessionId)
 
         // Start != 2
         waitAndClick(Locator.tagWithText("button", "Search"));
-        waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "field-label")).click();
-        waitForElement(Locator.tagWithText("li", "Start")).click();
+        waitForElement(Locator.tagWithAttribute("input", "aria-labelledby", "field-label")).click();
+        waitForElement(Locator.tagWithAttribute("div", "role", "listbox").child(Locator.tagWithText("div", "Start"))).click();
         waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "operator-label")).click();
         waitForElement(Locator.tagWithText("li", "!=")).click();
         waitForElement(Locator.tagWithId("input", "value-select-0")).sendKeys("2");
@@ -1737,8 +1738,8 @@ private void testLuceneSearchUI(String sessionId)
 
         // Start < 173
         waitAndClick(Locator.tagWithText("button", "Search"));
-        waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "field-label")).click();
-        waitForElement(Locator.tagWithText("li", "Start")).click();
+        waitForElement(Locator.tagWithAttribute("input", "aria-labelledby", "field-label")).click();
+        waitForElement(Locator.tagWithAttribute("div", "role", "listbox").child(Locator.tagWithText("div", "Start"))).click();
         waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "operator-label")).click();
         waitForElement(Locator.tagWithText("li", "<")).click();
         waitForElement(Locator.tagWithId("input", "value-select-0")).sendKeys("173");
@@ -1748,8 +1749,8 @@ private void testLuceneSearchUI(String sessionId)
 
         // Start > 502
         waitAndClick(Locator.tagWithText("button", "Search"));
-        waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "field-label")).click();
-        waitForElement(Locator.tagWithText("li", "Start")).click();
+        waitForElement(Locator.tagWithAttribute("input", "aria-labelledby", "field-label")).click();
+        waitForElement(Locator.tagWithAttribute("div", "role", "listbox").child(Locator.tagWithText("div", "Start"))).click();
         waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "operator-label")).click();
         waitForElement(Locator.tagWithText("li", ">")).click();
         waitForElement(Locator.tagWithId("input", "value-select-0")).sendKeys("502");
@@ -1759,8 +1760,8 @@ private void testLuceneSearchUI(String sessionId)
 
         // Start <= 440
         waitAndClick(Locator.tagWithText("button", "Search"));
-        waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "field-label")).click();
-        waitForElement(Locator.tagWithText("li", "Start")).click();
+        waitForElement(Locator.tagWithAttribute("input", "aria-labelledby", "field-label")).click();
+        waitForElement(Locator.tagWithAttribute("div", "role", "listbox").child(Locator.tagWithText("div", "Start"))).click();
         waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "operator-label")).click();
         waitForElement(Locator.tagWithText("li", "<=")).click();
         waitForElement(Locator.tagWithId("input", "value-select-0")).sendKeys("440");
@@ -1770,8 +1771,8 @@ private void testLuceneSearchUI(String sessionId)
 
         // Start >= 609
         waitAndClick(Locator.tagWithText("button", "Search"));
-        waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "field-label")).click();
-        waitForElement(Locator.tagWithText("li", "Start")).click();
+        waitForElement(Locator.tagWithAttribute("input", "aria-labelledby", "field-label")).click();
+        waitForElement(Locator.tagWithAttribute("div", "role", "listbox").child(Locator.tagWithText("div", "Start"))).click();
         waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "operator-label")).click();
         waitForElement(Locator.tagWithText("li", ">=")).click();
         waitForElement(Locator.tagWithId("input", "value-select-0")).sendKeys("609");
@@ -1782,10 +1783,10 @@ private void testLuceneSearchUI(String sessionId)
         // Ref Allele equals GAAAA
         waitForElement(Locator.tagWithText("span", "0.029"));
         waitAndClick(Locator.tagWithText("button", "Search"));
-        waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "field-label")).click();
-        waitForElement(Locator.tagWithText("li", "Ref Allele")).click();
+        waitForElement(Locator.tagWithAttribute("input", "aria-labelledby", "field-label")).click();
+        waitForElement(Locator.tagWithAttribute("div", "role", "listbox").child(Locator.tagWithText("div", "Ref Allele"))).click();
         waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "operator-label")).click();
-        waitForElement(Locator.tagWithText("li", "equals")).click();
+        waitForElement(Locator.tagWithText("li", "Equals")).click();
         waitForElement(Locator.tagWithId("input", "value-select-0")).sendKeys("GAAAA");
         waitAndClick(Locator.tagWithClass("button", "filter-form-select-button"));
         waitForElement(Locator.tagWithText("span", "4506"));
@@ -1794,10 +1795,10 @@ private void testLuceneSearchUI(String sessionId)
         // Impact equals HIGH
         waitForElement(Locator.tagWithText("span", "0.029"));
         waitAndClick(Locator.tagWithText("button", "Search"));
-        waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "field-label")).click();
-        waitForElement(Locator.tagWithText("li", "Impact on Protein Coding")).click();
+        waitForElement(Locator.tagWithAttribute("input", "aria-labelledby", "field-label")).click();
+        waitForElement(Locator.tagWithAttribute("div", "role", "listbox").child(Locator.tagWithText("div", "Impact on Protein Coding"))).click();
         waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "operator-label")).click();
-        waitForElement(Locator.tagWithText("li", "equals")).click();
+        waitForElement(Locator.tagWithText("li", "Equals")).click();
         waitForElement(Locator.tagWithId("input", "value-select-0")).sendKeys("HI");
         waitForElement(Locator.tagWithId("input", "value-select-0")).sendKeys(Keys.ENTER);
         waitAndClick(Locator.tagWithClass("button", "filter-form-select-button"));
@@ -1807,10 +1808,10 @@ private void testLuceneSearchUI(String sessionId)
         // Ref Allele does not equal A
         waitForElement(Locator.tagWithText("span", "0.029"));
         waitAndClick(Locator.tagWithText("button", "Search"));
-        waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "field-label")).click();
-        waitForElement(Locator.tagWithText("li", "Ref Allele")).click();
+        waitForElement(Locator.tagWithAttribute("input", "aria-labelledby", "field-label")).click();
+        waitForElement(Locator.tagWithAttribute("div", "role", "listbox").child(Locator.tagWithText("div", "Ref Allele"))).click();
         waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "operator-label")).click();
-        waitForElement(Locator.tagWithText("li", "does not equal")).click();
+        waitForElement(Locator.tagWithText("li", "Does Not Equal")).click();
         waitForElement(Locator.tagWithId("input", "value-select-0")).sendKeys("A");
         waitAndClick(Locator.tagWithClass("button", "filter-form-select-button"));
         waitForElement(Locator.tagWithText("span", "711"));
@@ -1819,10 +1820,10 @@ private void testLuceneSearchUI(String sessionId)
         // Alt Allele contains TT
         waitForElement(Locator.tagWithText("span", "0.029"));
         waitAndClick(Locator.tagWithText("button", "Search"));
-        waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "field-label")).click();
-        waitForElement(Locator.tagWithText("li", "Alt Allele")).click();
+        waitForElement(Locator.tagWithAttribute("input", "aria-labelledby", "field-label")).click();
+        waitForElement(Locator.tagWithAttribute("div", "role", "listbox").child(Locator.tagWithText("div", "Alt Allele"))).click();
         waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "operator-label")).click();
-        waitForElement(Locator.tagWithText("li", "contains")).click();
+        waitForElement(Locator.tagWithText("li", "Contains")).click();
         waitForElement(Locator.tagWithId("input", "value-select-0")).sendKeys("TT");
         waitAndClick(Locator.tagWithClass("button", "filter-form-select-button"));
         waitForElement(Locator.tagWithText("span", "22559"));
@@ -1831,10 +1832,10 @@ private void testLuceneSearchUI(String sessionId)
         // Alt Allele does not contain T
         waitForElement(Locator.tagWithText("span", "0.029"));
         waitAndClick(Locator.tagWithText("button", "Search"));
-        waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "field-label")).click();
-        waitForElement(Locator.tagWithText("li", "Alt Allele")).click();
+        waitForElement(Locator.tagWithAttribute("input", "aria-labelledby", "field-label")).click();
+        waitForElement(Locator.tagWithAttribute("div", "role", "listbox").child(Locator.tagWithText("div", "Alt Allele"))).click();
         waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "operator-label")).click();
-        waitForElement(Locator.tagWithText("li", "does not contain")).click();
+        waitForElement(Locator.tagWithText("li", "Does Not Contain")).click();
         waitForElement(Locator.tagWithId("input", "value-select-0")).sendKeys("T");
         waitAndClick(Locator.tagWithClass("button", "filter-form-select-button"));
         waitForElementToDisappear(Locator.tagWithText("span", "2"));
@@ -1843,10 +1844,10 @@ private void testLuceneSearchUI(String sessionId)
         // Ref Allele starts with GA
         waitForElement(Locator.tagWithText("span", "0.029"));
         waitAndClick(Locator.tagWithText("button", "Search"));
-        waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "field-label")).click();
-        waitForElement(Locator.tagWithText("li", "Ref Allele")).click();
+        waitForElement(Locator.tagWithAttribute("input", "aria-labelledby", "field-label")).click();
+        waitForElement(Locator.tagWithAttribute("div", "role", "listbox").child(Locator.tagWithText("div", "Ref Allele"))).click();
         waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "operator-label")).click();
-        waitForElement(Locator.tagWithText("li", "starts with")).click();
+        waitForElement(Locator.tagWithText("li", "Starts With")).click();
         waitForElement(Locator.tagWithId("input", "value-select-0")).sendKeys("GA");
         waitAndClick(Locator.tagWithClass("button", "filter-form-select-button"));
         waitForElement(Locator.tagWithText("span", "14716"));
@@ -1855,10 +1856,10 @@ private void testLuceneSearchUI(String sessionId)
         // Ref Allele ends with AAA
         waitForElement(Locator.tagWithText("span", "0.029"));
         waitAndClick(Locator.tagWithText("button", "Search"));
-        waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "field-label")).click();
-        waitForElement(Locator.tagWithText("li", "Ref Allele")).click();
+        waitForElement(Locator.tagWithAttribute("input", "aria-labelledby", "field-label")).click();
+        waitForElement(Locator.tagWithAttribute("div", "role", "listbox").child(Locator.tagWithText("div", "Ref Allele"))).click();
         waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "operator-label")).click();
-        waitForElement(Locator.tagWithText("li", "ends with")).click();
+        waitForElement(Locator.tagWithText("li", "Ends With")).click();
         waitForElement(Locator.tagWithId("input", "value-select-0")).sendKeys("AAA");
         waitAndClick(Locator.tagWithClass("button", "filter-form-select-button"));
         waitForElement(Locator.tagWithText("span", "4506"));
@@ -1866,30 +1867,30 @@ private void testLuceneSearchUI(String sessionId)
 
         // Alt Allele is empty
         waitAndClick(Locator.tagWithText("button", "Search"));
-        waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "field-label")).click();
-        waitForElement(Locator.tagWithText("li", "Alt Allele")).click();
+        waitForElement(Locator.tagWithAttribute("input", "aria-labelledby", "field-label")).click();
+        waitForElement(Locator.tagWithAttribute("div", "role", "listbox").child(Locator.tagWithText("div", "Alt Allele"))).click();
         waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "operator-label")).click();
-        waitForElement(Locator.tagWithText("li", "is empty")).click();
+        waitForElement(Locator.tagWithText("li", "Is Empty")).click();
         waitAndClick(Locator.tagWithClass("button", "filter-form-select-button"));
         waitForElement(Locator.tagWithText("span", "18235"));
         clearFilterDialog("alt is empty");
 
         // IMPACT is not empty
         waitAndClick(Locator.tagWithText("button", "Search"));
-        waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "field-label")).click();
-        waitForElement(Locator.tagWithText("li", "Impact on Protein Coding")).click();
+        waitForElement(Locator.tagWithAttribute("input", "aria-labelledby", "field-label")).click();
+        waitForElement(Locator.tagWithAttribute("div", "role", "listbox").child(Locator.tagWithText("div", "Impact on Protein Coding"))).click();
         waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "operator-label")).click();
-        waitForElement(Locator.tagWithText("li", "is not empty")).click();
+        waitForElement(Locator.tagWithText("li", "Is Not Empty")).click();
         waitAndClick(Locator.tagWithClass("button", "filter-form-select-button"));
         waitForElement(Locator.tagWithText("span", "914"));
         clearFilterDialog("IMPACT is not empty");
 
         // IMPACT HIGH+MODERATE
         waitAndClick(Locator.tagWithText("button", "Search"));
-        waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "field-label")).click();
-        waitForElement(Locator.tagWithText("li", "Impact on Protein Coding")).click();
+        waitForElement(Locator.tagWithAttribute("input", "aria-labelledby", "field-label")).click();
+        waitForElement(Locator.tagWithAttribute("div", "role", "listbox").child(Locator.tagWithText("div", "Impact on Protein Coding"))).click();
         waitForElement(Locator.tagWithAttribute("div", "aria-labelledby", "operator-label")).click();
-        waitForElement(Locator.tagWithText("li", "equals")).click();
+        waitForElement(Locator.tagWithText("li", "Equals")).click();
         waitForElement(Locator.tagWithId("input", "value-select-0")).sendKeys("HI");
         waitForElement(Locator.tagWithId("input", "value-select-0")).sendKeys(Keys.ENTER);
         waitForElement(Locator.tagWithId("input", "value-select-0")).sendKeys("MO");
@@ -1897,6 +1898,40 @@ private void testLuceneSearchUI(String sessionId)
         waitAndClick(Locator.tagWithClass("button", "filter-form-select-button"));
         waitForElement(Locator.tagWithText("span", "0.029"));
 
+        // Test the CSV export on this discrete case prior to clearing -- there should be 2 rows
+        File downloadCSV = doAndWaitForDownload(() -> clickButton("Export CSV", 0));
+        try (FileReader fileReader = new FileReader(downloadCSV))
+        {
+            CSVReader csvReader = new CSVReader(fileReader);
+            String[] line = csvReader.readNext();
+            Assert.assertArrayEquals(new String[] {
+                    "contig", "start", "end", "ref", "alt", "genomicPosition",
+                    "nCalled", "fractionHet", "variableSamples", "homozygousVarSamples",
+                    "nHomVar", "nHet", "AF", "AC", "CADD_PH", "CLN_ALLELE", "OMIMD", "IMPACT"
+            }, line);
+            line = csvReader.readNext();
+            Assert.assertArrayEquals(new String[] {
+                    "1", "2", "2", "A", "T", "2", "1523", "0.9268293",
+                    "m00004,m00013,m00029,m00101,m00391,m00435,m00458,m00598,m00610,m00789,m00801,m00816,m00969,m02168," +
+                            "m02169,m02179,m02225,m02230,m02280,m02324,m02344,m02369,m02391,m03592,m03655,m03667,m03669," +
+                            "m03684,m03694,m05192,m05264,m05270,m05273,m05550,m05551,m05557,m05622,m05640,m05658,m05659," +
+                            "m05660,m05662,m05666,m05668,m05669,m05671,m05672,m05673,m05675,m05795,m05812,m05834,m05855," +
+                            "m05861,m05895,m06088,m06969,m06970,m06985,m06986,m06988,m06993,m07003,m07006,m07007,m07025," +
+                            "m07034,m07037,m07045,m07409,m07418,m07426,m07438,m07446,m07458,m07489,m07495,m07513,m07863," +
+                            "m07929,m07951,m07952",
+                    "m03694,m05671,m05672,m06970,m06993,m07951",
+                    "6", "76", "0.029", "88", "7.292", "", "", "HIGH"
+            }, line);
+            line = csvReader.readNext();
+            Assert.assertArrayEquals(new String[] {
+                    "1","5336","5336","A","G","5336","1524","1.0","m05373","","0","1","3.281E-4","1","2.868","","","MODERATE"
+            }, line);
+        }
+        catch (Exception e)
+        {
+            Assert.fail();
+        }
+
         clearFilterDialog("IMPACT equals HIGH,MODERATE");
 
         testLuceneColumnSerialization(sessionId);
diff --git a/singlecell/resources/chunks/CustomUCell.R b/singlecell/resources/chunks/CustomUCell.R
index d1a958669..c5c9b0a02 100644
--- a/singlecell/resources/chunks/CustomUCell.R
+++ b/singlecell/resources/chunks/CustomUCell.R
@@ -25,7 +25,6 @@ for (datasetId in names(seuratObjects)) {
 
   seuratObj <- UCell::AddModuleScore_UCell(seuratObj, features = toCalculate, storeRanks = storeRanks, assay = assayName)
   corData <- RIRA::PlotUcellCorrelation(seuratObj, toCalculate)
-  saveRDS(corData, file = paste0(datasetId, '.ucellcorr.rds'))
 
   for (n in names(toCalculate)) {
     print(Seurat::FeaturePlot(seuratObj, features = paste0(n, '_UCell'), min.cutoff = 'q02', max.cutoff = 'q98'))
diff --git a/singlecell/resources/chunks/RunTricycle.R b/singlecell/resources/chunks/RunTricycle.R
new file mode 100644
index 000000000..b04162f1d
--- /dev/null
+++ b/singlecell/resources/chunks/RunTricycle.R
@@ -0,0 +1,12 @@
+ for (datasetId in names(seuratObjects)) {
+    printName(datasetId)
+    seuratObj <- readSeuratRDS(seuratObjects[[datasetId]])
+
+    seuratObj <- CellMembrane::RunTricycle(seuratObj)
+
+    saveData(seuratObj, datasetId)
+
+    # Cleanup
+    rm(seuratObj)
+    gc()
+}
\ No newline at end of file
diff --git a/singlecell/resources/queries/singlecell/samples.js b/singlecell/resources/queries/singlecell/samples.js
index 1a0d6d8f7..0b78206ec 100644
--- a/singlecell/resources/queries/singlecell/samples.js
+++ b/singlecell/resources/queries/singlecell/samples.js
@@ -62,4 +62,12 @@ function beforeUpsert(row, oldRow, errors){
     if (['Lung R', 'Lung Right', 'Lung-Right'].indexOf(row.tissue) !== -1){
         row.tissue = 'Lung-R';
     }
+
+    if (['Bulk', 'bulk'].indexOf(row.assaytype) !== -1){
+        row.assaytype = 'Bulk cells';
+    }
+
+    if (['Peptide Stim-BFA', 'Peptide stim-BFA'].indexOf(row.assaytype) !== -1){
+        row.assaytype = 'Peptide Stim - BFA';
+    }
 }
\ No newline at end of file
diff --git a/singlecell/resources/views/singleCellDataManagement.html b/singlecell/resources/views/singleCellDataManagement.html
index cfda8679e..0c0393de9 100644
--- a/singlecell/resources/views/singleCellDataManagement.html
+++ b/singlecell/resources/views/singleCellDataManagement.html
@@ -48,6 +48,18 @@
                     },{
                         name: 'cDNA Libraries with Hashing and Single HTO/Lane',
                         url: LABKEY.ActionURL.buildURL('query', 'executeQuery.view', null, {schemaName: 'singlecell', queryName: 'cdna_libraries', 'query.uniqueHtos~in': '0;1', 'query.hashingReadsetId/name~isnonblank': null, 'query.hashingReadsetId/totalFiles~eq': 0})
+                    },{
+                        name: 'GEX Readsets Missing Nimble (Measured using MHC)',
+                        url: LABKEY.ActionURL.buildURL('query', 'executeQuery.view', null, {
+                            schemaName: 'sequenceanalysis',
+                            queryName: 'sequence_readsets',
+                            'query.distinctOutputGenomes~contains': 'Mmul_10',
+                            'query.status~isblank': null,
+                            'query.totalForwardReads~isnonblank': null,
+                            'query.sort': 'rowid',
+                            'query.librarytype~eq': '10x 5\' GEX',
+                            'query.distinctOutputGenomes~doesnotcontain': 'Rhesus Macaque MHC v2'
+                        })
                     },{
                         name: 'Analyses In Novogene-Related Workbook',
                         url: LABKEY.ActionURL.buildURL('query', 'executeQuery.view', null, {schemaName: 'sequenceanalysis', queryName: 'sequence_analyses', 'query.container/title~containsoneof': 'Novogene;shipment'})
diff --git a/singlecell/src/org/labkey/singlecell/SingleCellController.java b/singlecell/src/org/labkey/singlecell/SingleCellController.java
index 5252fe424..3ad268982 100644
--- a/singlecell/src/org/labkey/singlecell/SingleCellController.java
+++ b/singlecell/src/org/labkey/singlecell/SingleCellController.java
@@ -21,10 +21,13 @@
 import org.apache.commons.lang3.StringUtils;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
+import org.jetbrains.annotations.NotNull;
 import org.json.JSONArray;
+import org.json.JSONObject;
 import org.labkey.api.action.ApiResponse;
 import org.labkey.api.action.ApiSimpleResponse;
 import org.labkey.api.action.ApiUsageException;
+import org.labkey.api.action.ConfirmAction;
 import org.labkey.api.action.ExportAction;
 import org.labkey.api.action.MutatingApiAction;
 import org.labkey.api.action.ReadOnlyApiAction;
@@ -45,9 +48,12 @@
 import org.labkey.api.module.Module;
 import org.labkey.api.module.ModuleHtmlView;
 import org.labkey.api.module.ModuleLoader;
+import org.labkey.api.pipeline.PipelineJobException;
 import org.labkey.api.query.BatchValidationException;
 import org.labkey.api.query.FieldKey;
+import org.labkey.api.query.InvalidKeyException;
 import org.labkey.api.query.QueryService;
+import org.labkey.api.query.QueryUpdateServiceException;
 import org.labkey.api.query.UserSchema;
 import org.labkey.api.security.RequiresPermission;
 import org.labkey.api.security.User;
@@ -58,19 +64,24 @@
 import org.labkey.api.sequenceanalysis.pipeline.PipelineStepProvider;
 import org.labkey.api.sequenceanalysis.pipeline.SequencePipelineService;
 import org.labkey.api.util.FileUtil;
+import org.labkey.api.util.HtmlString;
 import org.labkey.api.util.JsonUtil;
 import org.labkey.api.util.PageFlowUtil;
 import org.labkey.api.util.Path;
 import org.labkey.api.util.URLHelper;
+import org.labkey.api.view.HtmlView;
 import org.labkey.api.view.NavTree;
 import org.labkey.api.view.template.ClientDependency;
+import org.labkey.singlecell.analysis.AbstractSingleCellHandler;
 import org.labkey.singlecell.run.CellRangerWrapper;
 import org.springframework.validation.BindException;
+import org.springframework.validation.Errors;
 import org.springframework.web.servlet.ModelAndView;
 
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.IOException;
+import java.sql.SQLException;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collections;
@@ -558,4 +569,127 @@ public void setCombineHashingCite(boolean combineHashingCite)
             _combineHashingCite = combineHashingCite;
         }
     }
+
+    @RequiresPermission(AdminPermission.class)
+    public static class UpdatePrototypeDescriptionsAction extends ConfirmAction<Object>
+    {
+        @Override
+        public void validateCommand(Object form, Errors errors)
+        {
+
+        }
+
+        @Override
+        public @NotNull URLHelper getSuccessURL(Object form)
+        {
+            return getContainer().getStartURL(getUser());
+        }
+
+        @Override
+        public ModelAndView getConfirmView(Object form, BindException errors) throws Exception
+        {
+            return new HtmlView(HtmlString.unsafe("This will update the description field for all seurat prototypes. Do you want to continue?"));
+        }
+
+        @Override
+        public boolean handlePost(Object form, BindException errors) throws Exception
+        {
+            UserSchema sa = QueryService.get().getUserSchema(getUser(), getContainer(), SingleCellSchema.SEQUENCE_SCHEMA_NAME);
+            List<Map<String, Object>> toUpdate = new ArrayList<>();
+            new TableSelector(sa.getTable("outputfiles"), PageFlowUtil.set("rowid"), new SimpleFilter(FieldKey.fromString("category"), "Seurat Object Prototype").addCondition(FieldKey.fromString("modified"), "2025-04-29", CompareType.DATE_LT), null).forEach(Integer.class, rowId -> {
+                SequenceOutputFile so = SequenceOutputFile.getForId(rowId);
+                if (so == null)
+                {
+                    throw new IllegalStateException("Unable to create SequenceOutputFile for: " + rowId);
+                }
+
+                try
+                {
+                    JSONObject params = new JSONObject();
+
+                    String oldDescription = so.getDescription();
+                    if (oldDescription.contains("SoupX: true"))
+                    {
+                        params.put("singleCellRawData.PrepareRawCounts.useSoupX", true);
+                    }
+
+                    if (oldDescription.contains("Hashing: "))
+                    {
+                        List<String> matching = Arrays.stream(oldDescription.split("\n")).filter(x -> x.contains("Hashing: ")).toList();
+                        if (!matching.isEmpty())
+                        {
+                            if (matching.size() == 1)
+                            {
+                                params.put("singleCell.RunCellHashing.consensusMethods", matching.get(0).replaceFirst("Hashing: ", ""));
+                            }
+                            else
+                            {
+                                _log.error("Expected single match for Hashing on rowId: "+ rowId);
+                            }
+                        }
+                    }
+
+                    if (oldDescription.contains("Cite-seq Normalization: "))
+                    {
+                        List<String> matching = Arrays.stream(oldDescription.split("\n")).filter(x -> x.contains("Cite-seq Normalization: ")).toList();
+                        if (!matching.isEmpty())
+                        {
+                            if (matching.size() == 1)
+                            {
+                                params.put("singleCell.AppendCiteSeq.normalizeMethod", matching.get(0).replaceFirst("Cite-seq Normalization: ", ""));
+                            }
+                            else
+                            {
+                                _log.error("Expected single match for Cite-seq Normalization on rowId: "+ rowId);
+                            }
+                        }
+                    }
+
+                    String description = AbstractSingleCellHandler.getOutputDescription(params, _log, so.getFile(), null);
+                    toUpdate.add(new CaseInsensitiveHashMap<>(Map.of("rowid", so.getRowid(), "container", so.getContainer(), "description", description)));
+
+                    if (toUpdate.size() % 200 == 0)
+                    {
+                        doUpdate(toUpdate, getUser(), getContainer());
+                        toUpdate.clear();
+                    }
+                }
+                catch (PipelineJobException e)
+                {
+                    _log.error("Error generating description for: " + rowId, e);
+                }
+            });
+
+            if (!toUpdate.isEmpty())
+            {
+                doUpdate(toUpdate, getUser(), getContainer());
+                toUpdate.clear();
+            }
+
+            return true;
+        }
+    }
+
+    private static void doUpdate(List<Map<String, Object>> toUpdate, User u, Container c)
+    {
+        try
+        {
+            _log.info("Total prototype updates: " + toUpdate.size());
+
+            BatchValidationException bve = new BatchValidationException();
+            List<Map<String, Object>> oldKeys = toUpdate.stream().map(row -> Map.of("rowid", row.get("rowid"))).toList();
+
+            UserSchema sa = QueryService.get().getUserSchema(u, c, SingleCellSchema.SEQUENCE_SCHEMA_NAME);
+            sa.getTable("outputfiles").getUpdateService().updateRows(u, c, toUpdate, oldKeys, bve, null, null);
+
+            if (bve.hasErrors())
+            {
+                throw bve;
+            }
+        }
+        catch (SQLException | InvalidKeyException | QueryUpdateServiceException | BatchValidationException e)
+        {
+            _log.error("Unable to update outputfiles", e);
+        }
+    }
 }
diff --git a/singlecell/src/org/labkey/singlecell/SingleCellModule.java b/singlecell/src/org/labkey/singlecell/SingleCellModule.java
index 28d08146f..5559f897f 100644
--- a/singlecell/src/org/labkey/singlecell/SingleCellModule.java
+++ b/singlecell/src/org/labkey/singlecell/SingleCellModule.java
@@ -94,6 +94,7 @@
 import org.labkey.singlecell.pipeline.singlecell.RunScGate;
 import org.labkey.singlecell.pipeline.singlecell.RunScGateBuiltin;
 import org.labkey.singlecell.pipeline.singlecell.RunSingleR;
+import org.labkey.singlecell.pipeline.singlecell.RunTricycle;
 import org.labkey.singlecell.pipeline.singlecell.RunVision;
 import org.labkey.singlecell.pipeline.singlecell.ScoreCellCycle;
 import org.labkey.singlecell.pipeline.singlecell.SeuratPrototype;
@@ -297,6 +298,7 @@ public static void registerPipelineSteps()
         SequencePipelineService.get().registerPipelineStep(new RunDecoupler.Provider());
         SequencePipelineService.get().registerPipelineStep(new PerformDefaultNimbleAppend.Provider());
         SequencePipelineService.get().registerPipelineStep(new PerformMhcDimRedux.Provider());
+        SequencePipelineService.get().registerPipelineStep(new RunTricycle.Provider());
 
         SequenceAnalysisService.get().registerReadsetListener(new SingleCellReadsetListener());
     }
diff --git a/singlecell/src/org/labkey/singlecell/analysis/AbstractSingleCellHandler.java b/singlecell/src/org/labkey/singlecell/analysis/AbstractSingleCellHandler.java
index 5c63eed6f..6e9c2fb0d 100644
--- a/singlecell/src/org/labkey/singlecell/analysis/AbstractSingleCellHandler.java
+++ b/singlecell/src/org/labkey/singlecell/analysis/AbstractSingleCellHandler.java
@@ -616,7 +616,7 @@ else if (step.createsSeuratObjects())
                 so.setName(output.getDatasetName() == null ? output.getDatasetId() : output.getDatasetName());
                 so.setCategory("Seurat Object");
                 so.setFile(output.getFile());
-                String description = getOutputDescription(ctx, output.getFile(), List.of("Steps: " + steps.stream().map(x -> x.getProvider().getName()).collect(Collectors.joining("; "))));
+                String description = getOutputDescription(ctx.getParams(), ctx.getLogger(), output.getFile(), List.of("Steps: " + steps.stream().map(x -> x.getProvider().getName()).collect(Collectors.joining("; "))));
                 if (jobDescription != null)
                 {
                     description = jobDescription + "\n" + description;
@@ -986,7 +986,7 @@ public void serializeTest() throws Exception
         }
     }
 
-    public static String getOutputDescription(JobContext ctx, File seuratObj, @Nullable List<String> descriptions) throws PipelineJobException
+    public static String getOutputDescription(JSONObject jsonParams, Logger log, File seuratObj, @Nullable List<String> descriptions) throws PipelineJobException
     {
         if (descriptions == null)
         {
@@ -1015,6 +1015,18 @@ public static String getOutputDescription(JobContext ctx, File seuratObj, @Nulla
                 int hashingIdx = -1;
                 int saturationIdx = -1;
                 boolean hashingUsed = true;
+                int riraIdx = -1;
+                int traIdx = -1;
+                int trbIdx = -1;
+                int trdIdx = -1;
+                int trgIdx = -1;
+
+                int totalTNK = 0;
+                int cellsWithTRA = 0;
+                int cellsWithTRB = 0;
+                int cellsWithTRD = 0;
+                int cellsWithTRG = 0;
+                int cellsLackingCDR3 = 0;
                 while ((line = reader.readNext()) != null)
                 {
                     // This will test whether this is the first line or not
@@ -1023,12 +1035,17 @@ public static String getOutputDescription(JobContext ctx, File seuratObj, @Nulla
                         hashingIdx = Arrays.asList(line).indexOf("HTO.Classification");
                         if (hashingIdx == -1)
                         {
-                            ctx.getLogger().debug("HTO.Classification field not present, skipping");
+                            log.debug("HTO.Classification field not present, skipping");
                             hashingUsed = false;
                             hashingIdx = -2;
                         }
 
                         saturationIdx = Arrays.asList(line).indexOf("Saturation.RNA");
+                        traIdx = Arrays.asList(line).indexOf("TRA");
+                        trbIdx = Arrays.asList(line).indexOf("TRB");
+                        trdIdx = Arrays.asList(line).indexOf("TRD");
+                        trgIdx = Arrays.asList(line).indexOf("TRG");
+                        riraIdx = Arrays.asList(line).indexOf("RIRA_Immune_v2.cellclass");
                     }
                     else
                     {
@@ -1063,6 +1080,59 @@ else if ("NotUsed".equals(val))
                             double saturation = Double.parseDouble(line[saturationIdx]);
                             totalSaturation += saturation;
                         }
+
+                        if (riraIdx >= 0)
+                        {
+                            if ("T_NK".equals(line[riraIdx]))
+                            {
+                                boolean hasCDR3 = false;
+                                totalTNK++;
+                                if (traIdx >= 0)
+                                {
+                                    String tra = StringUtils.trimToNull(line[traIdx]);
+                                    if (tra != null && !"NA".equals(tra))
+                                    {
+                                        cellsWithTRA++;
+                                        hasCDR3 = true;
+                                    }
+                                }
+
+                                if (trbIdx >= 0)
+                                {
+                                    String trb = StringUtils.trimToNull(line[trbIdx]);
+                                    if (trb != null && !"NA".equals(trb))
+                                    {
+                                        cellsWithTRB++;
+                                        hasCDR3 = true;
+                                    }
+                                }
+
+                                if (trdIdx >= 0)
+                                {
+                                    String trd = StringUtils.trimToNull(line[trdIdx]);
+                                    if (trd != null && !"NA".equals(trd))
+                                    {
+                                        cellsWithTRD++;
+                                        hasCDR3 = true;
+                                    }
+                                }
+
+                                if (trgIdx >= 0)
+                                {
+                                    String trg = StringUtils.trimToNull(line[trgIdx]);
+                                    if (trg != null && !"NA".equals(trg))
+                                    {
+                                        cellsWithTRG++;
+                                        hasCDR3 = true;
+                                    }
+                                }
+
+                                if (!hasCDR3)
+                                {
+                                    cellsLackingCDR3++;
+                                }
+                            }
+                        }
                     }
                 }
 
@@ -1090,6 +1160,20 @@ else if ("NotUsed".equals(val))
                 {
                     descriptions.add("Mean RNA Saturation: " + (totalSaturation / (double) totalCells));
                 }
+
+                if (totalTNK > 0)
+                {
+                    descriptions.add("Total T/NK Cells: " + decimal.format(totalTNK));
+                    descriptions.add("% T/NK Cells with TRA: " + pf.format(cellsWithTRA / (double)totalTNK));
+                    descriptions.add("% T/NK Cells with TRB: " + pf.format(cellsWithTRB / (double)totalTNK));
+                    descriptions.add("% T/NK Cells with TRD: " + pf.format(cellsWithTRD / (double)totalTNK));
+                    descriptions.add("% T/NK Cells with TRG: " + pf.format(cellsWithTRG / (double)totalTNK));
+                    descriptions.add("% T/NK Cells without TCR: " + pf.format(cellsLackingCDR3 / (double)totalTNK));
+                }
+                else if (riraIdx == -1 || traIdx == -1)
+                {
+                    descriptions.add("TCR information not present");
+                }
             }
             catch (IOException e)
             {
@@ -1097,18 +1181,18 @@ else if ("NotUsed".equals(val))
             }
         }
 
-        if (ctx.getParams().optBoolean("singleCellRawData.PrepareRawCounts.useSoupX", false))
+        if (jsonParams.optBoolean("singleCellRawData.PrepareRawCounts.useSoupX", false))
         {
             descriptions.add("SoupX: true");
         }
 
-        String hashingMethods = ctx.getParams().optString("singleCell.RunCellHashing.consensusMethods");
+        String hashingMethods = jsonParams.optString("singleCell.RunCellHashing.consensusMethods");
         if (StringUtils.trimToNull(hashingMethods) != null)
         {
             descriptions.add("Hashing: " + hashingMethods);
         }
 
-        String citeNormalize = ctx.getParams().optString("singleCell.AppendCiteSeq.normalizeMethod");
+        String citeNormalize = jsonParams.optString("singleCell.AppendCiteSeq.normalizeMethod");
         if (StringUtils.trimToNull(citeNormalize) != null)
         {
             descriptions.add("Cite-seq Normalization: " + citeNormalize);
diff --git a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/RunTricycle.java b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/RunTricycle.java
new file mode 100644
index 000000000..5e059a782
--- /dev/null
+++ b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/RunTricycle.java
@@ -0,0 +1,39 @@
+package org.labkey.singlecell.pipeline.singlecell;
+
+import org.json.JSONObject;
+import org.labkey.api.sequenceanalysis.pipeline.AbstractPipelineStepProvider;
+import org.labkey.api.sequenceanalysis.pipeline.PipelineContext;
+import org.labkey.api.singlecell.pipeline.SeuratToolParameter;
+import org.labkey.api.singlecell.pipeline.SingleCellStep;
+
+import java.util.Arrays;
+
+public class RunTricycle extends AbstractCellMembraneStep
+{
+    public RunTricycle(PipelineContext ctx, RunTricycle.Provider provider)
+    {
+        super(provider, ctx);
+    }
+
+    public static class Provider extends AbstractPipelineStepProvider<SingleCellStep>
+    {
+        public Provider()
+        {
+            super("RunTricycle", "Run Tricycle", "CellMembrane/Tricycle", "This will run tricycle on the input object(s) to score cell cycle, and save the results in metadata.", Arrays.asList(
+
+            ), null, null);
+        }
+
+        @Override
+        public RunTricycle create(PipelineContext ctx)
+        {
+            return new RunTricycle(ctx, this);
+        }
+    }
+
+    @Override
+    public String getFileSuffix()
+    {
+        return "tricycle";
+    }
+}
diff --git a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/SeuratPrototype.java b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/SeuratPrototype.java
index 02c00c9d5..c7f1ccddf 100644
--- a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/SeuratPrototype.java
+++ b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/SeuratPrototype.java
@@ -145,7 +145,7 @@ public Output execute(SequenceOutputHandler.JobContext ctx, List<SeuratObjectWra
             String readsetName = ctx.getSequenceSupport().getCachedReadset(wrapper.getReadsetId()).getName();
             so.setReadset(wrapper.getReadsetId());
             so.setName(readsetName + ": Prototype Seurat Object");
-            so.setDescription(AbstractSingleCellHandler.getOutputDescription(ctx, so.getFile(), null));
+            so.setDescription(AbstractSingleCellHandler.getOutputDescription(ctx.getParams(), ctx.getLogger(), so.getFile(), null));
 
             ctx.getFileManager().addSequenceOutput(so);
         }
diff --git a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/VireoHandler.java b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/VireoHandler.java
index c3e432cf8..eb7ae055d 100644
--- a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/VireoHandler.java
+++ b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/VireoHandler.java
@@ -160,81 +160,102 @@ public void processFilesRemote(List<SequenceOutputFile> inputFiles, JobContext c
             }
             ctx.getFileManager().addIntermediateFile(barcodes);
 
-            List<String> cellsnp = new ArrayList<>();
-            cellsnp.add("cellsnp-lite");
-            cellsnp.add("-s");
-            cellsnp.add(bam.getPath());
-            cellsnp.add("-b");
-            cellsnp.add(barcodes.getPath());
-            cellsnp.add("--genotype");
+            Integer maxThreads = SequencePipelineService.get().getMaxThreads(ctx.getLogger());
+            ReferenceGenome genome = ctx.getSequenceSupport().getCachedGenome(inputFiles.get(0).getLibrary_id());
 
             File cellsnpDir = new File(ctx.getWorkingDirectory(), "cellsnp");
-            if (cellsnpDir.exists())
+            File cellsnpVcf = new File(cellsnpDir, "cellSNP.base.vcf.gz");
+            File cellsnpVcfIdx = new File(cellsnpVcf.getPath() + ".tbi");
+            if (cellsnpVcfIdx.exists())
             {
-                try
+                ctx.getLogger().info("cellsnp has already run, resuming");
+            }
+            else
+            {
+                List<String> cellsnp = new ArrayList<>();
+                cellsnp.add("cellsnp-lite");
+                cellsnp.add("-s");
+                cellsnp.add(bam.getPath());
+                cellsnp.add("-b");
+                cellsnp.add(barcodes.getPath());
+                cellsnp.add("--genotype");
+
+                if (cellsnpDir.exists())
                 {
-                    FileUtils.deleteDirectory(cellsnpDir);
+                    try
+                    {
+                        FileUtils.deleteDirectory(cellsnpDir);
+                    }
+                    catch (IOException e)
+                    {
+                        throw new PipelineJobException(e);
+                    }
                 }
-                catch (IOException e)
+
+                cellsnp.add("-O");
+                cellsnp.add(cellsnpDir.getPath());
+
+                if (maxThreads != null)
                 {
-                    throw new PipelineJobException(e);
+                    cellsnp.add("-p");
+                    cellsnp.add(maxThreads.toString());
                 }
-            }
 
-            cellsnp.add("-O");
-            cellsnp.add(cellsnpDir.getPath());
+                cellsnp.add("--minMAF");
+                cellsnp.add("0.1");
 
-            Integer maxThreads = SequencePipelineService.get().getMaxThreads(ctx.getLogger());
-            if (maxThreads != null)
-            {
-                cellsnp.add("-p");
-                cellsnp.add(maxThreads.toString());
-            }
+                cellsnp.add("--minCOUNT");
+                cellsnp.add("100");
 
-            cellsnp.add("--minMAF");
-            cellsnp.add("0.1");
+                String maxDepth = StringUtils.trimToNull(ctx.getParams().optString("maxDepth"));
+                if (maxDepth != null)
+                {
+                    cellsnp.add("--maxDEPTH");
+                    cellsnp.add(maxDepth);
+                }
 
-            cellsnp.add("--minCOUNT");
-            cellsnp.add("100");
+                cellsnp.add("--gzip");
 
-            String maxDepth = StringUtils.trimToNull(ctx.getParams().optString("maxDepth"));
-            if (maxDepth != null)
-            {
-                cellsnp.add("--maxDEPTH");
-                cellsnp.add(maxDepth);
-            }
+                cellsnp.add("--refseq");
+                cellsnp.add(genome.getWorkingFastaFile().getPath());
 
-            cellsnp.add("--gzip");
+                int vcfFile = ctx.getParams().optInt(REF_VCF, -1);
+                if (vcfFile > -1)
+                {
+                    File vcf = ctx.getSequenceSupport().getCachedData(vcfFile);
+                    if (vcf == null || !vcf.exists())
+                    {
+                        throw new PipelineJobException("Unable to find file with ID: " + vcfFile);
+                    }
 
-            ReferenceGenome genome = ctx.getSequenceSupport().getCachedGenome(inputFiles.get(0).getLibrary_id());
+                    cellsnp.add("-R");
+                    cellsnp.add(vcf.getPath());
+                }
+                else
+                {
+                    String contigs = ctx.getParams().optString("contigs", "");
+                    if (!StringUtils.isEmpty(contigs))
+                    {
+                        cellsnp.add("--chrom");
+                        cellsnp.add(contigs);
+                    }
+                }
 
-            cellsnp.add("--refseq");
-            cellsnp.add(genome.getWorkingFastaFile().getPath());
+                new SimpleScriptWrapper(ctx.getLogger()).execute(cellsnp);
 
-            int vcfFile = ctx.getParams().optInt(REF_VCF, -1);
-            if (vcfFile > -1)
-            {
-                File vcf = ctx.getSequenceSupport().getCachedData(vcfFile);
-                if (vcf == null || ! vcf.exists())
+                try
                 {
-                    throw new PipelineJobException("Unable to find file with ID: " + vcfFile);
-                }
+                    SequenceAnalysisService.get().ensureVcfIndex(cellsnpVcf, ctx.getLogger());
 
-                cellsnp.add("-R");
-                cellsnp.add(vcf.getPath());
-            }
-            else
-            {
-                String contigs = ctx.getParams().optString("contigs", "");
-                if (!StringUtils.isEmpty(contigs))
+                    File cellsVcf = new File(cellsnpDir, "cellSNP.cells.vcf.gz");
+                    SequenceAnalysisService.get().ensureVcfIndex(cellsVcf, ctx.getLogger());
+                }
+                catch (IOException e)
                 {
-                    cellsnp.add("--chrom");
-                    cellsnp.add(contigs);
+                    throw new PipelineJobException(e);
                 }
             }
 
-            new SimpleScriptWrapper(ctx.getLogger()).execute(cellsnp);
-
             List<String> vireo = new ArrayList<>();
             vireo.add("vireo");
             vireo.add("-c");
diff --git a/singlecell/src/org/labkey/singlecell/run/NimbleHelper.java b/singlecell/src/org/labkey/singlecell/run/NimbleHelper.java
index c33ed37c4..5dd635db4 100644
--- a/singlecell/src/org/labkey/singlecell/run/NimbleHelper.java
+++ b/singlecell/src/org/labkey/singlecell/run/NimbleHelper.java
@@ -538,7 +538,7 @@ public static File runNimbleReport(File alignResultsGz, int genomeId, PipelineSt
         reportArgs.add("-o");
         reportArgs.add(reportResultsGz.getPath());
 
-        runUsingDocker(reportArgs, output, null, ctx);
+        runUsingDocker(reportArgs, output, "nimble.report." + genomeId, ctx);
 
         if (!reportResultsGz.exists())
         {
@@ -566,7 +566,7 @@ public static File runNimbleReport(File alignResultsGz, int genomeId, PipelineSt
             plotArgs.add("--output_file");
             plotArgs.add(plotResultsHtml.getPath());
 
-            runUsingDocker(plotArgs, output, null, ctx);
+            runUsingDocker(plotArgs, output, "nimble.plot." + genomeId, ctx);
 
             if (!plotResultsHtml.exists())
             {