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I want to compare my vcf file to a vcf file supplied in the GATK bundle using Picard GenotypeConcordance. In the terminology used by Picard GenotypeConcordance I want to use a vcf file in the bundle as the "truth sample."
The problem is the vcf files in the bundle lack the sample name needed by Picard GenotypeConcordance.
That is, there is no value in these supplied vcf files to satisfy the Picard GenotypeConcordance required option:
TRUTH_SAMPLE (String) The name of the truth sample within the truth VCF Required.
Take dbsnp_138.hg19.vcf.gz as an example:
$ zcat dbsnp_138.hg19.vcf.gz | grep CHROM #CHROM POS ID REF ALT QUAL FILTER INFO
Based on the description of the vcf file format described elsewhere on this GATK site https://broadinstitute.org/gatk/guide/article?id=1268 I expect to see a FORMAT field and a sample name field following the INFO field.
How should I proceed?