COMPADRE

COMPADRE integrates genome-wide IBD sharing estimates from PRIMUS and shared segments length and distribution data from ERSA to improve relationship estimation accuracy in family networks ahead of pedigree generation. We aim to extend the number and variety of constructed pedigrees derived from populations with increased data heterogeneity.

You can read more about these individual methods in the original PRIMUS and ERSA manuscripts.

Updates

1. Added support for shared segments-based relationship estimation. This requires a file with pairwise shared segment data provided as input via the segment_data flag. We used GERMLINE2 in our benchmarking, but there are a large number of tools that can generate these data. File formatting examples for this input can be found in the example_data folder(s).

   --segment_data example_data/simulations/EUR/eur_size20_segments.txt

   Note: COMPADRE does not require segment-specific IBD[1/2] status as part of the --segment_data input; however, inclusion of this information can improve the composite algorithm's performance. We have provided a generic script to identify IBD2 segments from a standard IBD detection output file here: tools/determine_ibd.py. COMPADRE will check for the presence of an ibd column containing values 1 or 2 at the last index of the --segment_data input file.

2. Added support for using 1000 Genomes Project genetic reference data to generate pairwise IBD estimates.

Installation

Git: Click the green Code button at the top of this page and select a download option

Direct download: https://github.com/belowlab/compadre/archive/refs/heads/main.zip

Execution

We have provided a Dockerfile to help install dependencies and reference data ahead of running COMPADRE. First, however, you must install and launch the Docker client on your machine. Instructions to install Docker Engine on your system can be found here.

First, navigate into the compadre directory downloaded from Github:

# Assuming you cloned the repository in your current directory path
cd compadre

Copy your input data into the input folder (to be subsequently copied into the Docker image):

cp /example/local/data/folder/test.bed input/
cp /example/local/data/folder/test.bim input/
cp /example/local/data/folder/test.fam input/
cp /example/local/data/folder/segments.txt input/

Build the Docker image:

docker build -t compadre .

Run COMPADRE (interactive mode):

# Set entrypoint to bring you into the Docker image location
docker run -v /local/path/to/compadre_repo/output:/usr/src/output -p 6000:6000 -it --entrypoint /bin/bash compadre:latest 

# Run COMPADRE 
# (replace inputs with your own from the input/ folder)
perl run_COMPADRE.pl --file ../example_data/simulations/EUR/size20_0missing/eur_20_0 --segment_data ../example_data/simulations/EUR/eur_size20_segments.txt --genome --output ../output/eur_test --verbose 3

Run COMPADRE (non-interactive mode):

docker run -v /local/path/to/compadre_repo/output:/usr/src/output -p 6000:6000 compadre --file ../example_data/simulations/AMR/size20_0missing/amr_20_0 --segment_data ../example_data/simulations/AMR/amr_size20_segments.txt --genome --output ../output/amr_test --verbose 3

Execution notes

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• In order to easily access COMPADRE results on your local machine, use the -v flag in the Docker entrypoint step to link your local COMPADRE repository folder path (specifically, the output folder). For example, on macOS, this might be /Users/yourname/Downloads/compadre/output if you cloned the repository into your Downloads folder.
• Additional computation now takes place over an open socket, set to use port 6000 as default. If you need to use a different port, please indicate as such at runtime by using the --port_number=<INT> COMPADRE flag and the -p Docker flag.
• Please use standard PRIMUS runtime flags as detailed in the original PRIMUS documentation.

Additional Resources

The source code for generating family genetic data simulations can be found here.

More documentation:

• Original PRIMUS docs
• Original ERSA docs

Please visit the official COMPADRE website for publication updates and other details.

Questions?

Please email contact AT compadre DOT dev with the subject line "COMPADRE Help" or submit an issue report.

License

COMPADRE was developed by the Below Lab in the Division of Genetic Medicine at Vanderbilt University School of Medicine. COMPADRE is distributed under the following APACHE 2.0 license: https://compadre.dev/licenses/compadre_license.txt