What is the difference between -BadMateFilter and -MappingQualityFilter in Unifiedgenotyper?

leeyoungwha

It was a bit unclear what the BadMateFilter is doing in the documentation. Any information would be appreciated!

ebanks

Actually, that's not quite right (but it's not Geraldine's fault since the documentation in the code was wrong). The BadMateFilter removes reads whose mate maps to a different contig than it does.

Geraldine_VdAuwera

BadMateFilter applies to read pairs that are not properly paired or have mismatching information. MappingQualityFilter applies to reads that are assigned to a place on the reference with low confidence.