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:

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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)

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  • 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

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  • 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.
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