Bug Bulletin: The recent 3.2 release fixes many issues. If you run into a problem, please try the latest version before posting a bug report, as your problem may already have been solved.

Why are some of the annotation values different with VariantAnnotator compared to UG or HC?

Geraldine_VdAuweraGeraldine_VdAuwera Posts: 5,852Administrator, GATK Developer admin
edited August 2013 in FAQs

As featured in this forum question.

Two main things account for these kinds of differences, both linked to default behaviors of the tools:

  • The tools downsample to different depths of coverage

  • The tools apply different read filters

In both cases, you can end up looking at different sets or numbers of reads, which causes some of the annotation values to be different. It's usually not a cause for alarm. Remember that many of these annotations should be interpreted relatively, not absolutely.

Post edited by Geraldine_VdAuwera on

Geraldine Van der Auwera, PhD

Sign In or Register to comment.