ldgauthier
commented
3 years ago This is probably complicated by a bug in the htsjdk warning from previous versions, which should be fixed in the latest master now. There's probably still a bug, but the error will be more informative now.
There may be a ploidy-related bug since the somatic genotypes are a little funky that way. I don't like the fact that this is calling a biallelic method.
@fleharty if you still care about this, can you run it again with the latest master?
Riad900
tmelman
Bug Report
Affected tool(s) or class(es)
VariantAnnotator
Affected version(s)
Description
Throws an exception on a legal variant.
java.lang.IllegalStateException: Allele in genotype G not in the variant context [G*, G, GT] at htsjdk.variant.variantcontext.VariantContext$Validation.validateGenotypes(VariantContext.java:382) at htsjdk.variant.variantcontext.VariantContext$Validation.access$200(VariantContext.java:323) at htsjdk.variant.variantcontext.VariantContext$Validation$2.validate(VariantContext.java:331) at htsjdk.variant.variantcontext.VariantContext.lambda$validate$0(VariantContext.java:1384) at java.lang.Iterable.forEach(Iterable.java:75) at htsjdk.variant.variantcontext.VariantContext.validate(VariantContext.java:1384) at htsjdk.variant.variantcontext.VariantContext.(VariantContext.java:489)
at htsjdk.variant.variantcontext.VariantContextBuilder.make(VariantContextBuilder.java:647)
at htsjdk.variant.variantcontext.VariantContextBuilder.make(VariantContextBuilder.java:638)
at org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils.trimAlleles(GATKVariantContextUtils.java:1329)
at org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils.trimAlleles(GATKVariantContextUtils.java:1285)
at org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotatorEngine.getMinRepresentationBiallelics(VariantAnnotatorEngine.java:499)
at org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotatorEngine.annotateExpressions(VariantAnnotatorEngine.java:440)
at org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotatorEngine.annotateContext(VariantAnnotatorEngine.java:285)
at org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotator.apply(VariantAnnotator.java:230)
at org.broadinstitute.hellbender.engine.VariantWalker.lambda$traverse$0(VariantWalker.java:104)
at java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:184)
at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
at java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:175)
at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
at java.util.Iterator.forEachRemaining(Iterator.java:116)
at java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801)
at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481)
at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471)
at java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:151)
at java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:174)
at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:418)
at org.broadinstitute.hellbender.engine.VariantWalker.traverse(VariantWalker.java:102)
at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1048)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:139)
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:163)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:206)
at org.broadinstitute.hellbender.Main.main(Main.java:292)
I realize this is a open source project. But I've made copy of the failing VCF available at: /dsde/working/fleharty/tmp/buggy.vcf /dsde/working/fleharty/tmp/buggy.vcf.idx
Steps to reproduce
gatk VariantAnnotator -V buggy.vcf --resource:gnomad af-only-gnomad.raw.sites.vcf -E gnomad.AF --resource-allele-concordance -O gnomad_annotated.vcf
Expected behavior
Should work
Actual behavior
Throws exception