GATK

Genotyping with GATK is done in two pass. First, HaplotypeCaller is called on every sample using the option --ERC BP_RESOLUTION. The resulting gVCF file then contains the SNP calls plus the coverage at every position of the reference genome. Once every sample has been called with HaplotypeCaller, the gVCFs are merged (with CombineGVCFs) and the final vcf file is obtained with GenotypeGVCFs. Using --ERC BP_RESOLUTION enables us to keep the coverage information for each sample, at positions where SNPs were called in other samples. This information will be needed at the filtering step.

Simplified Directed Acyclic Graph (DAG) for GATK (HaplotypeCaller and GenotypeGVCFs) SNP calling and distance calculation