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Liftover gVCFs with indels #1280

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nh13 opened this issue Feb 13, 2019 · 4 comments
Open

Liftover gVCFs with indels #1280

nh13 opened this issue Feb 13, 2019 · 4 comments

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@nh13
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@nh13 nh13 commented Feb 13, 2019

I think that LiftoverVcf isn't working with a gVCF and indel allele in a reference block when trying to left-align indels.

Changing this line to catch if a.length == 0 gets me farther (back to this issue #1258):
https://github.com/broadinstitute/picard/blob/master/src/main/java/picard/util/LiftoverUtils.java#L370

Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: -1
    at picard.util.LiftoverUtils.lambda$leftAlignVariant$3(LiftoverUtils.java:370)
    at java.util.stream.Collectors.lambda$groupingBy$45(Collectors.java:907)
    at java.util.stream.ReduceOps$3ReducingSink.accept(ReduceOps.java:169)
    at java.util.HashMap$ValueSpliterator.forEachRemaining(HashMap.java:1620)
    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 picard.util.LiftoverUtils.leftAlignVariant(LiftoverUtils.java:370)
    at picard.util.LiftoverUtils.reverseComplementVariantContext(LiftoverUtils.java:172)
    at picard.util.LiftoverUtils.liftVariant(LiftoverUtils.java:81)
    at picard.vcf.LiftoverVcf.doWork(LiftoverVcf.java:396)
    at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:295)
    at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103)
    at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:113)
@yfarjoun

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@yfarjoun yfarjoun commented Feb 14, 2019

a.length() should never be zero...hmmm.

@tfenne

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@tfenne tfenne commented Feb 14, 2019

How long is a symbolic allele (e.g. <NON_REF>)?

@yfarjoun

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@yfarjoun yfarjoun commented Feb 15, 2019

zero.

I think that a VC with symbolic alleles should not be left-aligned...so a simple fix would be adding a check at the top of the left-align function and returning the input VC if it contains any symbolic alleles.

@AlbertoMaillo

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@AlbertoMaillo AlbertoMaillo commented May 28, 2019

Hi to all,

I am doing "lift over" from hg19 vcf to hg38 vcf. I use the chain file, obtained from: http://hgdownload.soe.ucsc.edu/goldenPath/hg19/liftOver/hg19ToHg38.over.chain
I have the same error and I have used the last version of picard(2.20.1). Someone could solve the problem?

Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: -1
at picard.util.LiftoverUtils.lambda$leftAlignVariant$3(LiftoverUtils.java:370)
*

Thanks!

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