Hi all, i am struggling a bit with preparing a cohort genome vcf file for joint genotyping using GATK.
I tried with 30 BAMs from 1000 genomes, and generated a single sample VCF for each, then used GATK CombineVariants and produced a "master" gVCF file.
This is not working during variant calling since it says the gVCF file is not valid.
Could someone please help in defining the right steps for generating a cohort gVCF file for use in GATK joint genotyping?
Thanks in advance.