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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.
Geraldine Van der Auwera, PhD