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Strange AD Value due to Select Variants

chongmchongm Member
edited January 2014 in Ask the GATK team

Hi,

I've used the Unified Genotyper for variant calling with GATK version 2.5.2. This was the info for a private variant.

GT:AD:DP:GQ:PL
0/1:52,37:88:99:1078,0,1486

However, after select variants to exclude non variant and variants not passing Filter, the AD changed and eliminated the alternative reads though the DP remained unchanged.

GT:AD:DP:GQ:PL
0/1:51,0:88:99:0,99,1283

I think I recall another post having a similar issue due to multithreaded use of select variants

http://gatkforums.broadinstitute.org/discussion/1943/weird-behaviour-of-selectvatiants

APologies for not commenting on this post instead as I had already posted this prior to seeing the other post!

Thanks,

MC

Post edited by chongm on

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