The current GATK version is 3.7-0
Examples: Monday, today, last week, Mar 26, 3/26/04

Howdy, Stranger!

It looks like you're new here. If you want to get involved, click one of these buttons!

Did you remember to?


1. Search using the upper-right search box, e.g. using the error message.
2. Try the latest version of tools.
3. Include tool and Java versions.
4. Tell us whether you are following GATK Best Practices.
5. Include relevant details, e.g. platform, DNA- or RNA-Seq, WES (+capture kit) or WGS (PCR-free or PCR+), paired- or single-end, read length, expected average coverage, somatic data, etc.
6. For tool errors, include the error stacktrace as well as the exact command.
7. For format issues, include the result of running ValidateSamFile for BAMs or ValidateVariants for VCFs.
8. For weird results, include an illustrative example, e.g. attach IGV screenshots according to Article#5484.
9. For a seeming variant that is uncalled, include results of following Article#1235.

Did we ask for a bug report?


Then follow instructions in Article#1894.

Formatting tip!


Surround blocks of code, error messages and BAM/VCF snippets--especially content with hashes (#)--with lines with three backticks ( ``` ) each to make a code block.
Powered by Vanilla. Made with Bootstrap.
Picard 2.9.0 is now available. Download and read release notes here.
GATK 3.7 is here! Be sure to read the Version Highlights and optionally the full Release Notes.

VariantEval on MultiSample calling VCF

thomas_wthomas_w MunichMember Posts: 17

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

Best Answer

Answers

  • thomas_wthomas_w MunichMember Posts: 17

    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.

  • pdexheimerpdexheimer Member, Dev Posts: 544 ✭✭✭✭

    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 Posts: 11,388 admin

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

    Geraldine Van der Auwera, PhD

Sign In or Register to comment.