bguo068/tskibd repository overview

tskibd is a tool designed to calculate Identity by Descent (IBD) segments from genealogical trees represented in the tree sequence format. It leverages the tskit C API library, which you can find at tskit repository.

⁠Usage

Pull the image:

docker pull bguo068/tskibd

Run without arguments (shows help message):

docker run --rm bguo068/tskibd

Run on local data: To allow the container to access your files, mount your current directory ($PWD) to the container volume:

docker run --rm -v $PWD:/data bguo068/tskibd 1 15000 150 2 example_data/chr1.trees

⁠Apptainer (Singularity)

You can also use Apptainer to build a .sif image directly from Docker (tested on Linux/amd64).

# Build the image
apptainer build ./tskibd.sif docker://bguo068/tskibd:v0.0.2

# Run the image
apptainer run ./tskibd.sif 1 15000 150 2 example_data/chr1.trees

⁠More information

Test data and more information is available at the https://github.com/bguo068/tskibd⁠