Hi,
I am running HaplotypeCaller -ERC GVCF for a cohort in parallel per sample per chromosome and combined the data using CombineGVCFs across the cohort on per chromosome basis. Can I run the GenotypeGVCFs to call variants across the cohort in parallel on all samples but per chromosome basis? follow by combining the vcf files using CatVariants or CombineVariants?
Thanks
Kin