Running Colocalization Analysis

1. Running with Probabilistic Fine-mapping Input

The command line syntax to run FastENLOC with the probabilistic fine-mapping input is

fastenloc -eqtl eqtl_annotation -gwas gwas_annotation -total_variants total_number_of_variants [-t tissue_name] 

Required options:

• -eqtl: specify the prepared eQTL annotation file
• -gwas: specify the prepared GWAS PIP file
• -total_variants: specify the number of genetic variants interrogated genome-wide
• -tissue: specify the tissue name (only required if multi-tissue eQTL annotation is used)

1.1 Running with Legacy GWAS Annotation Files

GWAS annotation files formatted for previous versions of FastENLOC remain compatible with newer versions (3.0 and above). To use these legacy-format files, specify the option -go gwas_input_legacy_format (instead of -gwas) to indicate the older GWAS annotation format.

2. Running with Summary Statistics Input

For combined summary statistics files, run colocalization analysis use the following command:

fastenloc -sum combined_summary_input_file -total_variants total_number_of_variants

where

• -sum: specify the combined summary statistics input file

3. Running with Hybrid Input

For hybrid input, where the eQTL file is in probabilistic fine-mapping format and the GWAS file is in summary statistics format, use the following command to run FastENLOC:

fastenloc -eqtl eqtl_annotation -gs gwas_summary_stats_file -total_variants total_number_variants [-t tissue_name]

Note that

• -gs: specify the summary statistics file containing only GWAS/complex trait information.