The current GATK version is 3.4-46

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# Multi-allelic sites being dropped in PhaseByTransmission?

Posts: 29Member

In switching to the 2.x series of GATK, I noticed that PBT now drops multi-allelic sites entirely from the output. Shouldn't the correct behavior be to write them out unmodified? Or is there a specific reason multi-allelic sites are not being written out?

Specifically, here is the current code

if (vc == null || !vc.isBiallelic())
return metricsCounters;


But I think it should be something like this...

if (vc == null)
return metricsCounters;
if (!vc.isBiallelic()) {
return metricsCounters;
}

Tagged:

Sorry to get to your question so late, it got dropped during a shift change.

I agree that it would make sense to write out multi-allelic sites as unmodified rather than drop them... I'll ask if the author of PBT, @Laurent, can shed some light on this.

Geraldine Van der Auwera, PhD