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Probable bug in SelectVariant --maxIndelSize

LaurentLaurent Member, Broadie

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

Best Answer

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    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)?

  • LaurentLaurent Member, Broadie

    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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