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README.md

Genomic Landscape of Structural Variation in Passer domesticus

Structural Variant Calling and Visual Curation

Snakefile #1: BWA alignment and GATK pipeline

Snakefile #2: Structural variant calling and genotyping with smoove(more here)

Intermediate steps needed prior to visual curation:

TO DO: JupyterNotebook for: Randomly selecting 3 individuals of each genotype (HOM_REF, HET, HOM_ALT) with gen_samplot.py for generating the Samplot images (.png) for PlotCritic

TO DO: Snakefile #3: Setting up a project in PlotCritic for visual curation, using SV-Plaudit on an Amazon Instance

Data Exploration

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.

Click to open Binder

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.

Click to open Binder

Notebook #2: Plotting Size Histograms for SVs

Click to open Binder

Notebook #3: Downsampling SNPs in PLINK and plotting PCAs to compare to similarly-sized SV-callsets

Click to open Binder

Notebook #4: Circos Plot in R Click to open Binder

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Structural Variant Analysis of short-read Illumina data for Passer domesticus

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