GLIMPSE Tools

Docker / Singularity

Usage

docker pull ghcr.io/signaturescience/glimpse
docker tag ghcr.io/signaturescience/glimpse glimpse

docker run --rm glimpse chunk
docker run --rm glimpse concordance
docker run --rm glimpse ligate
docker run --rm glimpse phase
docker run --rm glimpse sample
docker run --rm glimpse snparray
docker run --rm glimpse stats

Alternatively, use singularity:

singularity pull glimpse.sif docker://ghcr.io/signaturescience/glimpse

singularity run glimpse.sif chunk
singularity run glimpse.sif concordance
singularity run glimpse.sif ligate
singularity run glimpse.sif phase
singularity run glimpse.sif sample
singularity run glimpse.sif snparray
singularity run glimpse.sif stats

Build

git pull https://github.com/signaturescience/GLIMPSE
cd GLIMPSE
docker build --no-cache -t glimpse .

Versions

Current Release: 1.1.1. Release date: May 21, 2021

For details of past changes please see CHANGELOG.

License

GLIMPSE is available under a MIT license. For more information please see the LICENSE.

Features

GLIMPSE is a set of tools for phasing and imputation for low-coverage sequencing datasets:

• GLIMPSE_chunk splits the genome into chunks ready for imputation/phasing
• GLIMPSE_phase phases & imputes low coverage sequencing data
• GLIMPSE_ligate concatenates phased chunks of data into chromosome wide files
• GLIMPSE_sample allows sampling plausible haplotype configurations from the files

Documentation and tutorials

Please visit our website for tutorials, documentation and installation instructions:

https://odelaneau.github.io/GLIMPSE/