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variant QC graphs: bimodal QD
I'm trying to finalise good hard-filtering parameters. Does anyone know why the quality-by-depth distribution having has two peaks (See attached graphs, last column"QD").
This happens even after very strict filtering by basic metrics. There seems to be a lot of variants contributing to the two peaks so I'm guessing it's not due to a particular genomic region. (The graph lines are Drosophila chromosomes. Chr4 in blue is clearly poor. The Inbreeding coefficient and allele frequency are expected to be weird-looking due to our breeding design.)
Filter parameters are
(MQ > 61, MQ < 68, FS < 5, AN > 420, InbreedingCoeff > -1, DP < 10000, DP > 1000, ReadPosRankSum > -1, ReadPosRankSum < 1, ClippingRankSum > -.5, ClippingRankSum < .5, BaseQRankSum > -1, BaseQRankSum < 1, MQRankSum > -.5, MQRankSum < .5, EVENTLENGTH < 1, EVENTLENGTH > -1).