It looks like you're new here. If you want to get involved, click one of these buttons!
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 \<br />
-R ucsc.hg19.fasta \<br />
-T VariantEval \<br />
-o multisample.eval.gatkreport \<br />
--eval annotated.combined.vcf.gz \<br />
--dbsnp dbsnp_137.hg19.vcf<br />
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<br />
CompOverlap CompRod EvalRod JexlExpression Novelty nEvalVariants ...<br />
CompOverlap dbsnp eval none all 471704 191147<br />
CompOverlap dbsnp eval none known 280557 0<br />
CompOverlap dbsnp eval none novel 191147 191147<br />
But I would like to get one such entry per sample. Is there an easy way to do this?