This is the repo for "Phenome-wide Burden of Copy Number Variation in UK Biobank" (Aguirre MA, Rivas MAR, Priest JR, bioRxiv 2019). Contents of this repo are as below, in respective folders:
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constraint: Contains a Jupyter notebook which implements a null model of genic CNV used to estimate selective constraint, as well as scripts used to compute gene set enrichment analysis using the resulting constraint scores. -
figures: Contains notebooks used to generate figures and tables for the manuscript. -
genotypes: Contains scripts used to call CNVs using UK Biobank data, as well as a Jupyter notebook used to make the reference panel (available for download here, or on the Global Biobank Engine). -
gwas: Contains scripts used for genome-wide association of CNVs, and genic burden tests of CNVs. Summary stats available at the Global Biobank Engine link above.
Correspondence to Matthew Aguirre (magu) and James Priest (jpriest): username -at- stanford -dot- edu.