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Liftover gVCFs with indels

See original GitHub issue

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

Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: -1
    at picard.util.LiftoverUtils.lambda$leftAlignVariant$3(
    at java.util.HashMap$ValueSpliterator.forEachRemaining(
    at picard.util.LiftoverUtils.leftAlignVariant(
    at picard.util.LiftoverUtils.reverseComplementVariantContext(
    at picard.util.LiftoverUtils.liftVariant(
    at picard.vcf.LiftoverVcf.doWork(
    at picard.cmdline.CommandLineProgram.instanceMain(
    at picard.cmdline.PicardCommandLine.instanceMain(
    at picard.cmdline.PicardCommandLine.main(

Issue Analytics

  • State:closed
  • Created 5 years ago
  • Comments:9 (4 by maintainers)

github_iconTop GitHub Comments

yfarjouncommented, Feb 18, 2020

thanks for the test case @nh13

makes it much easier to debug!

yfarjouncommented, Feb 18, 2020

thanks @nh13

Read more comments on GitHub >

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