Benchmarking Pipeline for Enhancer Gene Links

This repository seeks to serve as one out of three parts of a Comparison Pipeline spearheaded by the ENCODE Consortium. In this module, we seek to compare enhancer gene links with common disease variants attained from two sources:

1. Fine-mapping inflammatory bowel disease loci to single-variant resolution (Huang et al 2017)
2. Fine-mapping in UK Biobank (Finucane et al): https://www.finucanelab.org/data

Getting Started

1. Create the conda environment via : conda env create -f workflow/envs/abc-max.yml
2. Activate the conda environment : conda activate abc-max

Downloading necessary input files

• hg19 ABC-Max Resources : http://mitra.stanford.edu/kundaje/kmualim/ABC_links/ABC-Max-Resources/ABC-Max-Resources.tar.gz
• ABC-Max-Resources.tar.gz file contains all the necessary input files to reproduce Fig 1a and Fig 1b in https://www.nature.com/articles/s41586-021-03446-x as well as additional files to run ABC-Max on the fine-mapping done in IBD (Huang et al.) and UK BioBank (Finucane et al)

Updating the config file

1. Modify the config file to your file paths, prediction table file and trait table file.
2. Description for main configuration input json fields are located here: https://docs.google.com/spreadsheets/d/1vf7JvtPHVBrDldiUypQKXl2QLOfKOcATjxjZcV5uZQY/edit?usp=sharing
   An example of this config file is located here: ABC-Max-pipeline/config/ABC-Max.example.json
   An example of this prediction table file is located here: ABC-Max-pipeline/config/ABC-Max.config-preds.tsv
   An example of this traits table file is located here: ABC-Max-pipeline/config/ABC-Max.config-traits.tsv
   

Customizing your own variant and credible set list files

Essential columns needed for the variant and credible set files located in ABC-Max-pipeline/config/ABC-Max.config-traits.tsv A description of the essential columns required for the variant and credible set files is located here: https://docs.google.com/spreadsheets/d/1xold84upBFigZPFQGUMeNC5t2id-Bub_Y1o5Xid_MHw/edit?usp=sharing

Running the pipeline

To run the pipeline, see ABC-Max-pipeline/workflow/run_snakemake.sh

• This is an example to run the pipeline for the Stanford Slurm Cluster To run it on your own computer, snakemake --snakefile Snakefile --configfile ../config/ABC-Max.example.json -j 1 --keep-target-files --rerun-incomplete

Example output files

Example output files are located ABC-Max-pipeline/tests