CatVariants Error - Features added out of order

ningboch

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:

ningboch

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)

Sheila

@ningboch
Hi,

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

Thanks,
Sheila

Geraldine_VdAuwera

CatVariants assumes that the files provided cover consecutive non-overlapping intervals. The error suggests this requirement is not satisfied in your dataset.