GATK 4.0.5.1 HaplotypeCaller Error: expected haplotypes.size() >= eventsAtThisLoc.size() + 1

Question

[sevvalakturk96]

Hi,

I was trying to call SNPs with HaplotypeCaller (GATK4.0.5.1) from multiple bam files (low coverage ancient human DNA). All the bam files includes Read Groups , were sorted ,and validated. I used emit all sites, genotype given alleles, min mapping quality, and min base quality arguments.

Here is my command :

 java -Xmx25g -jar  .../gatk-package-4.0.5.1-local.jar HaplotypeCaller -I Bam.list -R .../hs37d5.fa -L .../1000G.bed --output-mode EMIT_ALL_SITES --genotyping-mode GENOTYPE_GIVEN_ALLELES --alleles .../1000genome.phase3.vcf.gz --output xxx.vcf --minimum-mapping-quality 30 --min-base-quality-score 30

I got ERROR like this :

java.lang.IllegalArgumentException: expected haplotypes.size() >= eventsAtThisLoc.size() + 1
        at org.broadinstitute.hellbender.utils.Utils.validateArg(Utils.java:722)
        at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerGenotypingEngine.createAlleleMapper(AssemblyBasedCallerGenotypingEngine.java:158)
        at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerGenotypingEngine.assignGenotypeLikelihoods(HaplotypeCallerGenotypingEngine.java:143)
        at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerEngine.callRegion(HaplotypeCallerEngine.java:596)
        at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller.apply(HaplotypeCaller.java:248)
        at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.processReadShard(AssemblyRegionWalker.java:295)
        at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.traverse(AssemblyRegionWalker.java:271)
        at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:994)
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:135)
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:180)
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:199)
        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)

What could be the reason and solution for that? Any suggestions?

Thank you in advance.

[Ram]

Please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (`text` becomes text), or select a chunk of text and use the highlighted button to format it as a code block. I've done it for you this time.

[Pierre Lindenbaum]

current version is 4.1.6.0. Can you please try with a newer version.

[Pierre Lindenbaum]

java -Xmx25g -jar  .../gatk-package-4.0.5.1-local.jar

I don't think gatk should be lauched by invoking the jar directly.