covid-crispr-eqtl

Integration of genome-scale CRISPR loss-of-function screens and eQTLs in diverse cell types and tissues to pinpoint genes underlying COVID-19 risk in the 3p21.31 locus

This repository contains code to conduct the analyses presented in the article "Integrative approach identifies SLC6A20 and CXCR6 as putative causal genes for the COVID-19 GWAS signal in the 3p21.31 locus" (Kasela et al., 2021, Genome Biol, see the preprint in medRxiv).

Overview of this repository

• crispr_genes - script to explore the top-ranked genes from the CRISPR screen from Daniloski et al. 2021, Cell
• covid_gwas - scripts to perform inflation of COVID-19 GWAS signal for variants that are cis-eQTLs in Lung
• eqtl_coloc - scripts to perform colocalization analysis of molQTLs and COVID-19 GWAS signal in the the 3p21.31 locus
• ldsc - scripts to run the LDSC pipeline