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UnifiedGenotyper: different -glm values result in different annotated values
I have run UnifiedGenotyper with the -glm options SNP and BOTH. These two approaches yield identical variants and identical genotype likelihoods (at least the first 100k variants I checked). However, a few of the annotations have different values:
-glm SNP on the left and -glm BOTH on the right:
Why is that?
I noticed another user got different variants, but I get the same variants and the same likelihoods:
I ran single threaded.
I use MQRankSum and ReadPosRankSum for VariantRecalibrator, so it affects my downstream results, if the annotations are -glm dependent. Hence I am asking my question. I hope you can illuminate me. Thank you.