I am attempting to call exomes using GATK 3.8, the new quality model, and AS annotations. However, for chrX, I get an ArrayIndexOutOfBoundsException for chrX, likely as I am using different ploidy for males and females.
INFO 20:01:42,079 ProgressMeter - X:140994551 3505.0 30.0 s 2.4 h 1.9% 26.9 m 26.4 m
ERROR --
ERROR stack trace
java.lang.ArrayIndexOutOfBoundsException: 24
at org.broadinstitute.gatk.tools.walkers.genotyper.GeneralPloidyGenotypeLikelihoods.getNumLikelihoodElements(GeneralPloidyGenotypeLikelihoods.java:440)
at org.broadinstitute.gatk.tools.walkers.genotyper.GeneralPloidyGenotypeLikelihoods.subsetToAlleles(GeneralPloidyGenotypeLikelihoods.java:339)
at org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.IndependentAllelesExactAFCalculator.subsetAlleles(IndependentAllelesExactAFCalculator.java:494)
at org.broadinstitute.gatk.tools.walkers.genotyper.GenotypingEngine.calculateGenotypes(GenotypingEngine.java:292)
at org.broadinstitute.gatk.tools.walkers.genotyper.UnifiedGenotypingEngine.calculateGenotypes(UnifiedGenotypingEngine.java:392)
at org.broadinstitute.gatk.tools.walkers.genotyper.UnifiedGenotypingEngine.calculateGenotypes(UnifiedGenotypingEngine.java:375)
at org.broadinstitute.gatk.tools.walkers.genotyper.UnifiedGenotypingEngine.calculateGenotypes(UnifiedGenotypingEngine.java:330)
at org.broadinstitute.gatk.tools.walkers.variantutils.GenotypeGVCFs.regenotypeVC(GenotypeGVCFs.java:327)
at org.broadinstitute.gatk.tools.walkers.variantutils.GenotypeGVCFs.map(GenotypeGVCFs.java:305)
at org.broadinstitute.gatk.tools.walkers.variantutils.GenotypeGVCFs.map(GenotypeGVCFs.java:136)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:267)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:255)
at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:274)
at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:144)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:92)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:48)
at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:98)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:323)
at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:123)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:256)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:158)
at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:108)