Why are some of the annotation values different with VariantAnnotator compared to Unified Genotyper?

Geraldine_VdAuwera

As featured in this forum question.

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

1. The tools downsample to different depths of coverage

2. 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.