MMP::io

Tool to merge many GWAS summary statistics into one file ready to use in MMP.

Documentation for users: Download, Configure and Run.

Want to contribute to the code? Chek the section For developers.

For users

Download

1. Make and go to a directory for MMP::io files, for example:

   mkdir ~/mmpio
   cd ~/mmpio

2. Download mmpio from the release page

3. Move it to the current mmpio directory you created in (1.):

   mv ~/Downloads/mmpio-macos-arm64.tar .

4. Extract the archive:

   tar -xf mmpio-macos-arm64.tar

Configure

Still in the mmpio directory you created in (1.), do:

1. Copy config.json.sample to config.json

2. Edit config.json with name, paths and columns for each of your datasets

3. Specify groups of input files to be used for heterogeneity testing.

Run

Your current directory should now be the mmpio directory created in (1.) and it should contain the files mmpio and config.json.

Still in the mmpio directory you created in (1.), do:

./mmpio

This outputs a mmp.tsv file ready for upload on MMP.

Note

macOS users: You may need an extra step to run the downloaded mmpio binary due to macOS security settings.

Here is how to allow running the mmpio binary:

xattr -d com.apple.quarantine /path/to/downloaded/mmpio

For developers

Requirements

In order to make changes to the mmpio program, you need to have the following:

1. The Go programming language. Installation instructions here: https://go.dev/doc/install

Building

To build the mmpio binary:

1. Clone this git repository.
2. Go to the src directory within this repository.
3. Run go build -v to make the mmpio binary.