/vcpipe

variant calling pipeline for cicilid fish

Primary LanguagePython

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