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Variation between GATK runs
Dear gatk team,
I've read that HC produces somewhat non-deterministic results but these are older posts and I wanted to check if that's still the case for version 126.96.36.199 (in gvcf mode). Also, I wanted to know if that's the case for Mutect2 as well (also version 188.8.131.52).
I get slight variations - depending on the sample varying from 0.0004% to 0.01% according to vcf-compare (position-only comparision). The quality values vary more but I haven't looked into this in detail. I noticed that the differences between the runs increase after hard filtering for Mutect2 calls and decrease slightly for HC calls.
Is this to be expected or something to worry about?