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gatk4.1 FilterMutectCalls with java error "java.lang.NumberFormatException"

I use gatk4.1 mutect2 do tumor somatic analysis. When I used FilterMutectCalls to filter my raw.mutect2.vcf, a java error appeared: "java.lang.NumberFormatException".
The error information is :

java.lang.NumberFormatException: For input string: "."
at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)
at java.lang.Integer.parseInt(Integer.java:569)
at java.lang.Integer.valueOf(Integer.java:766)
at htsjdk.variant.variantcontext.CommonInfo.lambda$getAttributeAsIntList$1(CommonInfo.java:287)
at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
at java.util.Collections$2.tryAdvance(Collections.java:4717)
at java.util.Collections$2.forEachRemaining(Collections.java:4725)
at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481)
at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471)
at java.util.stream.ReduceOps$ReduceOp.evaluateSequential(ReduceOps.java:708)
at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:499)
at htsjdk.variant.variantcontext.CommonInfo.getAttributeAsList(CommonInfo.java:273)
at htsjdk.variant.variantcontext.CommonInfo.getAttributeAsIntList(CommonInfo.java:281)
at htsjdk.variant.variantcontext.VariantContext.getAttributeAsIntList(VariantContext.java:738)
at org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2FilteringEngine.applyReadPositionFilter(Mutect2FilteringEngine.java:223)
at org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2FilteringEngine.calculateFilters(Mutect2FilteringEngine.java:529)
at org.broadinstitute.hellbender.tools.walkers.mutect.FilterMutectCalls.firstPassApply(FilterMutectCalls.java:130)
at org.broadinstitute.hellbender.engine.TwoPassVariantWalker.lambda$traverseVariants$0(TwoPassVariantWalker.java:76)
at java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:184)
at java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:175)
at java.util.Iterator.forEachRemaining(Iterator.java:116)
at java.util.Spliterators$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.TwoPassVariantWalker.traverseVariants(TwoPassVariantWalker.java:74)
at org.broadinstitute.hellbender.engine.TwoPassVariantWalker.traverse(TwoPassVariantWalker.java:27)
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 reduce the number of raw.mutect2.vcf file and redo filter to find the wrong line location.
Then I find a line cause this error :
there is a "MPOS=.;" in the INFO field of the raw.mutect2.vcf file.

Why mutect2 result appear this error info? Please check it, thanks!

Answers

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