Multi-allelic sites being dropped in PhaseByTransmission?
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Comments (4)

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()) {
    vcfWriter.add(vc);
    return metricsCounters;
}

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