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Which part of mym QD plot is the homozygous peak?
Just a quick question, which I think may be of use to people with similarly...squiffy...plots! I've plotted out QD values v Density so as to inform the hard filtering process but I'm having difficulty discerning the expected peaks for heterozygous calls and homozygous calls, as described at https://software.broadinstitute.org/gatk/guide/article?id=6925. As you can see from the attached plot, there is a peak at the lower values (or is it a shoulder?), a tiny bump and then a major peak, but then just a shoulder on the other side of the peak. As filtering effectively (and stringently) is key to my study, I'd like to know what each peak and shoulder represents before I take the plunge if anyone can make an educated guess, please?