Variant Calling pipeline

Description

This snakemake pipeline is designed for Variant Calling

Inputs

• the bam files
• output directory
• reference genome
• SNP database
• bed file

Outputs

• logs\ - Directory of log files for each job, check here first if you run into errors
• working\ - Directory containing intermediate files for each job

Workflow

1. **genome_prepare
2. **BQSR--BaseRecalibrator, ApplyBQSR
3. **HaplotypeCaller--HaplotypeCaller
4. **JointCallSNPs--JointCallSNP, GenotypeGVCFs, GatherVcfs
5. **VQSR--VariantRecalibrator, ApplyVQSR

Setup environment

1. Install conda

2. Clone workflow into working directory

   git clone <repo> <dir>
   cd <dir>

3. Create a new enviroment

   conda env create -n <project> --file environment.yaml

4. Activate the environment

   conda activate <project_name>

5. Enable the Bioconda channel

   conda config --add channels bioconda
   conda config --add channels conda-forge
   

   !!!Notice conda default channel will cause SSL error with Max Planck intranet.

6. Install snakemake

   conda install snakemake

7. Edit configuration files change the path of fastq_dir, output_dir, reference_genome in "config.yaml"

8. Create index for your SNP database

   gatk IndexFeatureFile -I dbSNP.vcf.gz

9. The first time you are executing this snakemake pipeline it should run locally, once the first run is over (you can use --dry), you can switch to running it on the cluster.

   snakemake --configfile "config.yaml" --use-conda  --cores N --dryrun

10. Execute the workflow (Add the --notemp flag if you want to keep the intermediate files instead of automatically deleting them)

    snakemake --configfile "config.yaml" --use-conda  --cores N

if you need to submit the jobs to SGE cluster to run the pipeline

download snakemake-executor-plugin-cluster-generic by pip
```bash
pip install snakemake-executor-plugin-cluster-generic
```
then
```bash
snakemake --use-conda --jobs {cores}  --executor cluster-generic --cluster-generic-submit-cmd  "qsub -cwd -V -l h_vmem={resources.mem_mb}M  -pe parallel {threads} -o logs/ -e logs/"
```