Examining the Impact of Imputation Errors on Fine-Mapping Using DNA Methylation QTL as a Model Trait - Chundru et al. GENETICS 2019

This repository contains a pipeline to run the three Fine-mapping approaches (BIMBAM, BSLMM, and the J-test) and obtain credible sets from each.

Prerequistes

• BIMBAM: http://www.haplotype.org/bimbam.html
• GEMMA: https://github.com/genetics-statistics/GEMMA
  • gsl
  • lapack
• GCTA: http://cnsgenomics.com/software/gcta/index.html
• R
• python3
• plink

Running the methods

• Edit the paths at the begining of the file run.sh
• comment out any parts you don't wish to run in the run.sh file
• execute the run.sh file

Result files

• output/foo.jtest.credsets is the credible set from the J-test
• output/foo.bimbam.credsets is the credible set from BIMBAM
• output/foo.bslmm.credsets is the credible set from the BSLMM

Please feel free to contact me if you have any questions