mutect2-nf

GATK4 mutect2 test for missing variants in NGS composite run

setup

Clone this repository from GitHub:

git clone --recursive https://github.com/varshini712/mutect2-nf.git
cd mutect2-nf

usage

Make sure you have your container image files and reference files created/specified in your working dir. Use Makefile in this repo to submit job to slurm

Installs nextflow

make install

Submits sbatch job to slurm

make submit