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Meaning of error: expected haplotypes.size() >= eventsAtThisLoc.size() + 1

mrooneymrooney Cambridge, MAMember

Hi, I am running HaplotypeCaller (GATK in genoype-given-alleles mode using a VCF of common coding germline variants. Please see the error below. Can anyone help to point me in the right direction? Thanks!

java.lang.IllegalArgumentException: expected haplotypes.size() >= eventsAtThisLoc.size() + 1
at org.broadinstitute.hellbender.utils.Utils.validateArg(
at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.processReadShard(
at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.traverse(
at org.broadinstitute.hellbender.engine.GATKTool.doWork(
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(
at org.broadinstitute.hellbender.Main.runCommandLineProgram(
at org.broadinstitute.hellbender.Main.mainEntry(
at org.broadinstitute.hellbender.Main.main(



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