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Variation between GATK runs

JulsJuls Member ✭✭

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 (in gvcf mode). Also, I wanted to know if that's the case for Mutect2 as well (also version

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?

Thank you!!

Best Answer


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