Hi!
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.
#:GATKReport.v1.1:8
#:GATKTable:11:3:%s:%s:%s:%s:%s:%d:%d:%d:%.2f:%d:%.2f:;
#: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?
Thanks, Thomas
