Question: GATK joint genotyping
gravatar for win
2.3 years ago by
win840 wrote:

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.

ngs gatk • 1.3k views
ADD COMMENTlink written 2.3 years ago by win840

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?

ADD REPLYlink written 2.3 years ago by h.mon30k
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