GATK-pipeline

November 30, 2014 · View on GitHub

A shell script which implements GATK pipeline for variant calling. Creates a GVCF file for a sample BAM file. The GVCF files created by running the script on a cohort of samples can be jointly genotyped using GenotypeGVCFs

Download GATK from https://www.broadinstitute.org/gatk/download

Information on GATK - https://www.broadinstitute.org/gatk/

Dependencies

PicardTools
SAMtools

Usage

sh GATK.sh

Output

file_name_output.raw.snps.indels.g.vcf

GATK.pdf contains the explanation of the mathematics behind GATK-HaplotypeCaller.