GATK

I'm running into an error when running GATK 4.1.0.0 with the following call:

java -Xmx16g -jar ${gatkDir}/GATK.jar Mutect2 -R ${GRC}.fa -I ${TU}.recal.bam -tumor TU -I ${NM}.recal.bam -normal NM --native-pair-hmm-threads $threads --germline-resource $gnomad --af-of-alleles-not-in-resource 0.0000025 -O ${sampleName}.mutect.UF.vcf --tmp-dir temp

The error is as follows:

java.lang.IndexOutOfBoundsException: Index: 0, Size: 0
at java.util.ArrayList.rangeCheck(ArrayList.java:657)
at java.util.ArrayList.get(ArrayList.java:433)
at org.broadinstitute.hellbender.tools.walkers.mutect.GermlineProbabilityCalculator.lambda$getGermlineAltAlleleFrequencies$3(GermlineProbabilityCalculator.java:55)
at java.util.stream.ReferencePipeline$6$1.accept(ReferencePipeline.java:244)
at java.util.ArrayList$ArrayListSpliterator.forEachRemaining(ArrayList.java:1382)
at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481)
at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471)
at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:545)
at java.util.stream.AbstractPipeline.evaluateToArrayNode(AbstractPipeline.java:260)
at java.util.stream.DoublePipeline.toArray(DoublePipeline.java:506)
at org.broadinstitute.hellbender.tools.walkers.mutect.GermlineProbabilityCalculator.getGermlineAltAlleleFrequencies(GermlineProbabilityCalculator.java:57)
at org.broadinstitute.hellbender.tools.walkers.mutect.GermlineProbabilityCalculator.getNegativeLog10PopulationAFAnnotation(GermlineProbabilityCalculator.java:29)
at org.broadinstitute.hellbender.tools.walkers.mutect.SomaticGenotypingEngine.callMutations(SomaticGenotypingEngine.java:165)
at org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2Engine.callRegion(Mutect2Engine.java:233)
at org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2.apply(Mutect2.java:232)
at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.processReadShard(AssemblyRegionWalker.java:291)
at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.traverse(AssemblyRegionWalker.java:267)
at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:966)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:138)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:191)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:210)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:162)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:205)
at org.broadinstitute.hellbender.Main.main(Main.java:291)

I have seen errors like this listed before on the forums relating to the AF file. I removed the file, and it was able to successfully run. The AF file is af-only-gnomad.filtered.hg38.vcf.gz

However, the above function call with the AF file runs correctly on GATK 4.0.10.1 with no errors and completes successfully.

The AF file is formatted as follows:

#CHROM POS ID REF ALT QUAL FILTER INFO
1 10067 . T TAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCC 30.35 PASS .
1 10108 . CAACCCT C 46514.3 PASS .
1 10109 . AACCCT A 89837.3 PASS .
1 10114 . TAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCTAACCCTAACCCTAACCCTAACCCTAACCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCTAACCCTAACCCTAAACCCTA CAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCTAACCCTAACCCTAACCCTAACCCTAACCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCTAACCCTAACCCTAAACCCTA,T 36729 PASS .
1 10119 . CT C 251.23 PASS .
1 10120 . T C 14928.7 PASS .
1 10128 . ACCCTAACCCTAACCCTAAC A 285.71 PASS .
1 10131 . CT C 378.93 PASS .
...

Any thoughts as to what the error could be?

Thank you!