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Deletion QC plots
I'm inspecting my results from the Genomestrip/2.0 deletion pipeline: 244 of them reported on one 23Mb chromosome in 221 flies, at 20-40X coverage.
Attached is a density distribution plot for all of the quantitative metric in the final vcf.
I'm considering excluding variants that are in the tails of the distributions for coherence, depth p-value, maybe for the pairs measurements, and maybe outer left and right.
What do you reckon?
I'm also going to have quick look at a few of the pile-ups using Intergrated Genomics Viewer.