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Official code repository for GATK versions 4 and up
https://software.broadinstitute.org/gatk
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Enabling PDHMM causes GVCF mode to fail. #9041

Open gokalpcelik opened 1 week ago

gokalpcelik commented 1 week ago

Hi team.

Enabling --use-pdhmm true for HaplotypeCaller results in the below error message thrown when -ERC GVCF is enabled. 

java.lang.IllegalArgumentException: refHaplotype cannot be null
    at org.broadinstitute.hellbender.utils.Utils.nonNull(Utils.java:643)
    at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReferenceConfidenceModel.calculateRefConfidence(ReferenceConfidenceModel.java:216)
    at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerEngine.callRegion(HaplotypeCallerEngine.java:1018)
    at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller.apply(HaplotypeCaller.java:284)
    at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.processReadShard(AssemblyRegionWalker.java:200)
    at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.traverse(AssemblyRegionWalker.java:173)
    at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1119)
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:150)
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:203)
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:222)
    at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:166)
    at org.broadinstitute.hellbender.Main.mainEntry(Main.java:209)
    at org.broadinstitute.hellbender.Main.main(Main.java:306)

This happens under 4.6.0.0 and 4.6.1.0. I have not tested older versions.