The set of scripts in this repo are intended to generate the necessary input files and run programs to identify expression QTLs for RNA sequencing data using two programs: mixQTL (https://github.com/liangyy/mixqtl/wiki) and a QTLtools-based (https://qtltools.github.io/qtltools/) pipeline to incorporate local ancestry into the model. If you use these scripts for your own work, please cite our manuscript: https://www.medrxiv.org/content/10.1101/2023.02.09.23285622v1
This is a brief overview of our study design, which involved two methods (inferred local ancestry adjustment with permuted effect estimates generated with QTLtools and a combined haplotype-specific expression and total read count regression estimates generated with mixQTL) to identify expression QTLs in human coronary artery, as well as a separate analysis of splicing QTLs also performed with QTLtools. QTL identification was followed by various fine-mapping and annotation efforts utilizing the scripts in the respectively named folders. Links to tools used should be included in all scripts.
For questions regarding scripts or implementation, please email Chani at ch2um at virginia dot edu.