How to merge genotype info from multiple samples into 1 vcf with only 1 genotype column - VariantRec

dilawerkh4dilawerkh4 Member
edited August 2017 in Ask the GATK team

Hi everyone,

How do you at Broad merge genotype info from multiple samples into 1 vcf with only 1 genotype column, because I noticed your resource files used in VariantRecalibrator are formatted this way (resource bundle), and I assume this is the only acceptable way to use a vcf as a training or truth resource.

I tried combining genotype info from multiple samples using both:
CombineVariants, and
Vcftools merge-vcf

But in both cases the merged vcf had multiple genotype columns, one for each input sample. I assume this would not be an acceptable format to use as a training or truth resource in VariantRecalibrator.

Thanks in advance.

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