GATK joint genotyping

Question

[win]

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.

[h.mon]

Which version of GATK? What were the commands you used? Did you read the documentation (e.g here, here and here)? Did you name your gVCF as file.g.vcf?