Liftover gVCFs with indels
See original GitHub issueI 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 https://github.com/broadinstitute/picard/issues/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)
Issue Analytics
- State:
- Created 5 years ago
- Comments:9 (4 by maintainers)
Top Results From Across the Web
Functional equivalence of genome sequencing analysis ...
We tested pairwise variability in SNV, indel and SV callsets ... Next, GVCFs from all 100 samples were merged with GATK CombineGVCFs.
Read more >dbSNP 155 Track Settings - UCSC Genome Browser
We performed liftover using the GATK release 4.1.9 LiftoverVcf (Picard Version 2.23.3) tool with the default parameters. This successfully lifts over variants ...
Read more >Combining variants from different files into one - Google Sites
I called variants using Haplotype caller > gVCFs > GenotypedGVCFs. I then merged all the samples together using combineVariants tool. Now I have...
Read more >gnomAD v3.1 New Content, Methods, Annotations, and Data ...
The package includes functions to help users handle sparse Matrix Tables, annotate variants with VEP, lift over sites from GRCh37 to GRCh38 ...
Read more >Modules » nf-core
Call germline SNPs and indels via local re-assembly of haplotypes. Input. meta input input_index intervals ... liftOver. convert between genome builds.
Read more >
Top Related Medium Post
No results found
Top Related StackOverflow Question
No results found
Troubleshoot Live Code
Lightrun enables developers to add logs, metrics and snapshots to live code - no restarts or redeploys required.
Start Free
Top Related Reddit Thread
No results found
Top Related Hackernoon Post
No results found
Top Related Tweet
No results found
Top Related Dev.to Post
No results found
Top Related Hashnode Post
No results found
thanks for the test case @nh13
makes it much easier to debug!
thanks @nh13