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VariantEval on MultiSample calling VCF

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:
<br /> 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.

<br /> &#35;:GATKReport.v1.1:8<br /> &#35;:GATKTable:11:3:%s:%s:%s:%s:%s:%d:%d:%d:%.2f:%d:%.2f:;<br /> &#35;: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?

Thanks,
Thomas

Best Answer

Answers

  • thomas_wthomas_w MunichMember

    Thanks, I'll give it a try! I tried that one already yesterday, but in combination with some other modules and it said it would take something like 6 days. But with your combination the running time seems to be reasonable.

    However, I would like to get some more information on the single modules, but the links on the [gatkforums.broadinstitute.org/discussion/48/using-varianteval](manual page) don't work.

  • Yeah, I don't think there's ever been real comprehensive documentation on them - they kind of fall into that low-priority class with ROD Codecs and VariantAnnotator annotations. I've had pretty good success figuring things out through a combination of source diving and experimentation, though that obviously takes some time and effort

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    That's right, unfortunately they've just not been a priority -- those links are placeholders for when we eventually get around to documenting them.

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