Probable bug in SelectVariant --maxIndelSize

Laurent

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

Geraldine_VdAuwera

Hi Laurent,

This is actually a bug -- it should be counting deletions too. Unfortunately this will have to be fo the next release (2.5). Thanks for bringing this to our attention!

Geraldine_VdAuwera

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)?

Laurent

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