VariantCalling Pipe

Bash Script and Snakefile to call variations using GATK

Dependency

• picard
• gatk
• samtools
• snakemake

Usage

1. Run cfg.py to generate config.json for Snakefile
2. Run snakemake --cores N to do variant calling (N is required for running on lsf) 

cfg.py

python cfg.py wd DIR SUFFIX KEY  # add files through wildcard
python cfg.py ad KEY VALUE # add files through their paths 

snakefile

snakemake --cores N