Run GenotypeGVCFs by populations separately or all populations together ?

Guillaume_DGuillaume_D Lausanne, SwitzerlandMember

Hi GATK team,

I have a question about joint genotyping which I think has not been addressed yet in this forum. I want to do population genomics on a non model species. Once I have my gVCFs files for each individual of my five populations, should I run GenotypeGVCFs in all the individuals of each population separately or in all the individuals of all populations together? And if the 2nd solution is the correct one, is there a way to specify the population so that GenotypeGVCFs takes it into account?

Thanks in advance
Guillaume

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