GATK-pipeline
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
Usage
sh GATK.sh
Output
file_name_output.raw.snps.indels.g.vcf
GATK.pdf contains the explanation of the mathematics behind GATK-HaplotypeCaller.