parallel runs in genotypegvcfs ?

KinMokKinMok LondonMember

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

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