The Frontline Support team will be offline December 17-18 due to an institute-wide retreat and offline December 22- January 1, while the institute is closed. Thank you for your patience during these next few weeks as we get to all of your questions. Happy Holidays!
Run GenotypeGVCFs by populations separately or all populations together ?
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