Notice:
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.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.
Attention:
We will be out of the office on October 14, 2019, due to the U.S. holiday. We will return to monitoring the forum on October 15.

CatVariants Error - Features added out of order

ningbochningboch ✭ChinaMember ✭
in Ask the GATK team

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:

· Share on Twitter Share on Google+

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)

    · Share on Twitter Share on Google+
  • SheilaSheila admin 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

    · Share on Twitter Share on Google+
  • Geraldine_VdAuweraGeraldine_VdAuwera admin 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.
    · Share on Twitter Share on Google+
Sign In or Register to comment.