Snakefile: BWA alignment and GATK pipeline
Followed by: Structural variant calling and genotyping with smoove(more here)
JupyterNotebooks for executing all steps, from extracting curated variants from raw PlotCritic reports to final plotting in Python3. These need to be run in the order presented below.
Notebook #1, Part 1: Intersecting and plotting a PCA for all Deletions that were given "Yes" by all four curators.
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Notebook #1, Parts 2 to 4: Intersecting and plotting a PCA for all Deletions that were given either "Yes" or "Maybe" by all four curators; plotting all of the remaining SVs that were rejected by all four curators; and plotting all raw Uncurated Deletions.
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Notebook #2: Plotting Size Histograms for SVs
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Notebook #3: Downsampling SNPs in PLINK and plotting PCAs to compare to similarly-sized SV-callsets
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Notebook #4: Circos Plot in R
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