CreateSomaticPanelOfNormals fails

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Dieter Best

• February 28, 2020 23:46

Can you please provide
a) GATK version used
b) Exact GATK commands used
c) The entire error log if applicable.

Commandline: 

java -jar gatk.jar CreateSomaticPanelOfNormals --output pon.vcf.gz --vcfs normals.list

I am getting the following error. Any ideas what might be going on?

 

java.lang.IllegalStateException: The elements of the input Iterators are not sorted according to the comparator htsjdk.variant.variantcontext.VariantContextComparator
at htsjdk.samtools.util.MergingIterator.next(MergingIterator.java:113)
at org.broadinstitute.hellbender.tools.walkers.mutect.CreateSomaticPanelOfNormals.doWork(CreateSomaticPanelOfNormals.java:176)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:139)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:192)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:211)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)
at org.broadinstitute.hellbender.Main.main(Main.java:289)

 

 

 

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• 

  Bhanu Gandham

  • March 02, 2020 19:31

  Hi Dieter Best

  1. Looks like one of the input vcfs in your normals.list is not sorted. Can you check for that please?
  2. If the above is not the issue then how were the vcfs produced? Mutect2 should not produce unsorted vcf.  If you are using Mutect2 to produce these vcfs then please provide pipeline you are using

   

   

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  Dieter Best

  • March 03, 2020 18:16

  Thanks for responding so quickly.

  The bam files were produced with Mutect2 from GATK version 4.0.11.0

  The vcf files are in fact NOT sorted.

  I solved the problem with "picard SortVcf".

  Thanks.

   

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