Notice:
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We appreciate your help!

Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

CatVariants Error - Features added out of order

I am running the practices pipeline on a large set of WGS data. On some of the CatVariants steps I am getting errors with the GATK v3.5.
there are errors:

Answers

  • ningbochningboch ChinaMember

    java.lang.IllegalArgumentException: Features added out of order: previous (TabixFeature{referenceIndex=1, start=137479353, end=137479353, featureStartFilePosition=449144530967927, featureEndFilePosition=-1}) > next (TabixFeature{referenceIndex=1, start=28, end=28, featureStartFilePosition=449144530970244, featureEndFilePosition=-1})
    at htsjdk.tribble.index.tabix.TabixIndexCreator.addFeature(TabixIndexCreator.java:89)
    at htsjdk.variant.variantcontext.writer.IndexingVariantContextWriter.add(IndexingVariantContextWriter.java:170)
    at htsjdk.variant.variantcontext.writer.VCFWriter.add(VCFWriter.java:219)
    at org.broadinstitute.gatk.tools.CatVariants.execute(CatVariants.java:296)
    at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
    at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
    at org.broadinstitute.gatk.tools.CatVariants.main(CatVariants.java:312)

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @ningboch
    Hi,

    Can you please post the exact command you ran? How did you generate the VCF files?

    Thanks,
    Sheila

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin
    CatVariants assumes that the files provided cover consecutive non-overlapping intervals. The error suggests this requirement is not satisfied in your dataset.
Sign In or Register to comment.