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Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
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.