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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/"
```