gpu-coloc

gpu-coloc is an accelerated implementation of the coloc.bf_bf Bayesian colocalization algorithm (Chris Wallace, "A more accurate method for colocalisation analysis allowing for multiple causal variants", PLOS Genetics, 2021, coloc GitHub), delivering identical results to R's coloc.bf_bf approximately 1000 times faster (Also on CPUs!). For GPU-acceleration Torch support is required, thus gpu-coloc can be used on M-series Mac(book)s and machines with NVIDIA GPUs.

If you have any questions or problems with gpu-coloc, please write to mihkel.jesse@gmail.com.

Citation

If you use gpu-coloc, please cite: https://doi.org/10.1101/2025.08.25.672103

All of eQTL Catalogue ready for use with gpu-coloc can be found here.

Installation

Install via pip (Python ≥3.12):

pip install gpu-coloc

If pip cannot find the package, it is probably do to an older version of pip. Thus to upgrade it run:

pip install --upgrade pip

You can set up gpu-coloc up in a virtual environment:

python -m venv [path_to_venv]
source [path_to_venv]/bin/activate
pip install gpu-coloc

This is prefered in production environments or if you are having trouble with package management.

Verify Installation

To confirm installation, clone this repository:

git clone https://github.com/mjesse-github/gpu-coloc
cd gpu-coloc
bash test.sh

This creates an example/ directory containing an example_results.tsv file.

Workflow

Note: Paths assume gpu-coloc is in the working directory; adjust paths if necessary.

Variant Naming Convention

Variants must follow the naming format: chr[chromosome]_[position]_[ref]_[alt]. Ensure renaming is completed before Step 1. Use chromosome X, not 23.

1. Prepare Signals and Summary Files

Signal Files: Save signals as [signal].pickle, containing variants and their log Bayes Factors (lbf).

Example format:

variant	chrX_153412224_C_A	chrX_153412528_C_T	...
lbf	-0.060991	-1.508802	...

Summary File: Tab-separated, structured as:

signal	chromosome	location_min	location_max	signal_strength	lead_variant
QTD000141_ENSG00000013563_L1	X	153412224	155341332	12.1069377174147	chrX_154403855_T_G
...

Naming examples:

Summary: gwas_summary.tsv
Signals directory: gwas_signals/[signal].pickle

See scripts in summary_and_signals_examples/ for reference; modifications may be necessary.

2. Format Data

gpu-coloc --format --input [path_to_signals] --input_summary [summary_file] --output [output_folder]

Parameters for `gpu-coloc --format`

--input (required): Path to the directory containing signal files (e.g., gwas_signals/). Supports pickle or feather files (see --input_type).
--output (required): Path to the output directory where formatted parquet files will be saved.
--input_summary (required): Path to the summary TSV file (e.g., gwas_summary.tsv).
--output_summary (optional): Path to write the formatted summary as a parquet file.
--input_type (optional): Type of input files, either 'pickle' (default) or 'feather'.

3. Run Colocalization

gpu-coloc --run --dir1 [formatted_dataset_1] --dir2 [formatted_dataset_2] --results [results_output] --p12 1e-6 --H4 0.8

Parameters for `gpu-coloc --run`

--dir1 (required): Path to the first formatted dataset directory.
--dir2 (required): Path to the second formatted dataset directory.
--results (required): Path to the output file where colocalization results will be saved.
--p12 (optional): Prior probability that a variant is associated with both traits. Default: 1e-6.
--H4 (optional): Posterior probability threshold for declaring colocalization (H4). Default: 0.8.

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