- Perform single-sample germline variant calling with GATK HaplotypeCaller and the GATK GVCF workflow on exome data
- Perform joint genotype calling on exome data, including additional exomes from 1000 Genomes Project
- Manipulate and Filter VCFs to remove artifacts and identify variants of interest
In this module we will use the GATK HaplotypeCaller to call germline variants from "normal" bams. For a more in-depth look, see this excellent GATK tutorial, provided by the Broad Institute.