The Frontline Support team will be slow to respond December 17-18 due to an institute-wide retreat and offline December 22- January 1, while the institute is closed. Thank you for your patience during these next few weeks. Happy Holidays!
Strange AD Value due to Select Variants
I've used the Unified Genotyper for variant calling with GATK version 2.5.2. This was the info for a private variant.
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.
I think I recall another post having a similar issue due to multithreaded use of select variants
APologies for not commenting on this post instead as I had already posted this prior to seeing the other post!