simrub/glimpse repository overview

⁠GLIMPSE

⁠Versions

Current release: v2.0.0. Release date: Dec 07, 2022

For details of past changes please see CHANGELOG⁠.

⁠License

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

⁠Features

GLIMPSE2 is a set of tools for phasing and imputation for low-coverage sequencing datasets:

• GLIMPSE2_chunk splits the genome into chunks for imputation and phasing
• GLIMPSE2_split_reference creates the reference panel representation used by GLIMPSE2_phase. It allows major speedups for large reference panels.
• GLIMPSE2_phase program to impute and phase low coverage sequencing data
• GLIMPSE2_ligate concatenates phased chunks of data into chromosome-wide phased files

⁠Documentation and tutorials

Visit our website for tutorials, documentation and installation instructions:

https://odelaneau.github.io/GLIMPSE/⁠

⁠GLIMPSE1

At the moment, GLIMPSE2 performs imputation only from a reference panel of samples. To use the joint-model, particularly useful for many samples at higher coverages (>0.5x) and small reference panels, please visit the GLIMPSE1 website and checkout the GLIMPSE1 branch⁠.

⁠Installation

To build the source code, please refer to the step-by-step guide on the website⁠.

To run and test the pre-made docker images, you can run the following:

⁠GLIMPSE v2.0.0:

wget https://github.com/odelaneau/GLIMPSE/releases/download/v2.0.0/glimpse_v2.0.0-27-g0919952_20221207.tar.gz
docker load < glimpse_v2.0.0-27-g0919952_20221207.tar.gz
# test docker run using -it
docker run -it glimpse:v2.0.0-27-g0919952_20221207

To run the tools you can use 'GLIMPSE2_[tool name]' (e.g. GLIMPSE2_phase) inside the docker run (-it) session

⁠GLIMPSE v1.1.1:

wget https://github.com/odelaneau/GLIMPSE/releases/download/v1.1.1/glimpse_v1.1.1-c27e90d_20210521.tar.gz
docker load < glimpse_v1.1.1-c27e90d_20210521.tar.gz
# test docker run using -it
docker run -it glimpse:v1.1.1-c27e90d_20210521

To run the tools you can use 'GLIMPSE_[tool name]_v1.1.1' (e.g. GLIMPSE_phase_v1.1.1) inside the docker run (-it) session