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VariantEval on MultiSample calling VCF

thomas_wthomas_w Posts: 14Member


I want to know what's the best way to use VariantEval to get statistics for each sample in a multisample VCF file. If I call it like this:

java -jar GenomeAnalysisTK.jar \
-R ucsc.hg19.fasta \
-T VariantEval \
-o multisample.eval.gatkreport \
--eval annotated.combined.vcf.gz \
--dbsnp dbsnp_137.hg19.vcf

where annotated.combined.vcf.gz is a VCF file that contains ~1Mio variants for ~800 samples I get statistics for all samples combined, e.g.

#:GATKTable:CompOverlap:The overlap between eval and comp sites
CompOverlap CompRod EvalRod JexlExpression Novelty nEvalVariants ...
CompOverlap dbsnp eval none all 471704 191147

CompOverlap dbsnp eval none known 280557 0
CompOverlap dbsnp eval none novel 191147 191147

But I would like to get one such entry per sample. Is there an easy way to do this?


Best Answer


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