Bug Bulletin: we have identified a bug that affects indexing when producing gzipped VCFs. This will be fixed in the upcoming 3.2 release; in the meantime you need to reindex gzipped VCFs using Tabix.

Probable bug in SelectVariant --maxIndelSize

LaurentLaurent Posts: 33Member, GSA Collaborator

Dear All,

Just thought I should report a possible small bug with SelectVariant --maxIndelSize as I think it's only filtering insertions greater than the given value and not deletions. Of course using JEXL expressions I can still get the variants I'm after...

Cheers, Laurent

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Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 5,260Administrator, GSA Member admin

    Hi Laurent,

    Thanks for pointing this out, we'll take a look at what's going on there. Are you using the latest version (2.4-7)?

    Geraldine Van der Auwera, PhD

  • LaurentLaurent Posts: 33Member, GSA Collaborator

    Hi Geraldine,

    Yes, I am using 2.4-7. To be entirely fair, it could be debated whether this is the desired behavior (as deletions would be of negative length when compared to the reference genome) but maybe it could be specified in the documentation then. Also the fact that there is no --minIndelSize option got me thinking the the --maxIndelSize would perform size selection on both insertions and deletions.

    Cheers, Laurent

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