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Hard-Filtering odd MQ distributions
I'm working on filtering my snp calls from a non-model organism and thus going with hard-filtering instead of VQSR. I know this is always a bit of touch-and-go and there's no definite answer to which thresholds to employ (I've been through the documentation) but I'm hoping you can give me some more pointers.
I've started by using your indications first except for QD, and based on missing data and coverage. So right now I have filtered SNPs with: QD < 5 ¦¦ FS < 60 ¦¦ MQ < 40 ¦¦ MQRankSum < -12.5 ¦¦ ReadPosRankSum < -8 ¦¦ SOR < 3, maximum 30% missing calls, resulting in 16'397'726 SNPs (of 19'047'259 total unfiltered calls).
These the distributions before and after filtering (QUAL just for indication, didn't apply any filter to it).
It looks considerable better to me, but still far from what your example data looks like. In particular, I'm wondering about my MQ distribution that has these very high values (over 400, some come as "Inf" even) - have you seen this before?
Further, would it be "ok" to filter on the upper value of MQ as well as the lowest? Thanks !