Expression quantitative trait loci (eQTL) and fine-mapping analysis of a cohort from the 1000 Genomes Project using both lower coverage and higher coverage (30x) data.
The raw VCF data can be obtained from the 1000 Genomes Project: https://www.internationalgenome.org/data
The gene expression data can be obtained from the BioStudies website for the RNA-sequencing 1KGP paper: https://www.ebi.ac.uk/biostudies/arrayexpress/studies/E-GEUV-1/sdrf?full=true
The analysis is a little bit different when running on at-scale versus test data, leading to different files between them. To run this code on the test data: python run.py test. The test code will produce the QQ-plots and fine-mapping plots from the test data in the repository directory. The QQ plot will be in output_qqplot_test.pdf and the fine-mapping plots will be in the Rplots.pdf file. To run this code on the real data: python run.py all
This repository uses plink (https://www.cog-genomics.org/plink/1.9/), Matrix eQTL (http://www.bios.unc.edu/research/genomic_software/Matrix_eQTL/), susieR (https://github.com/stephenslab/susieR), and UCSC LiftOver (https://genome.ucsc.edu/cgi-bin/hgLiftOver). Check them out!
Thanks for stopping by this repository! :)