GATK joint genotyping
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.
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Jeremy Leipzig
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win
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win
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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?