GLIMPSE

RGlimpse2 fork

This repository preserves the upstream GLIMPSE2 source tree and adds a nested RGlimpse2/ R package. The package builds the pinned in-tree executables against the single htslib supplied by Rduckhts and performs runtime selection among scalar, AVX2, AVX-512, or NEON phase binaries. See the RGlimpse2 package documentation for the R API and installation contract. Downstream native changes are recorded in the audited patches/ series; concise future targets live in dev-notes/. The original GLIMPSE2 documentation follows below.

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.

Building from source

GLIMPSE2 supports Linux x86_64, Linux aarch64, and macOS ARM64 (Apple Silicon).

macOS (Apple Silicon)

brew install htslib boost libdeflate
git clone --recursive https://github.com/odelaneau/GLIMPSE.git
cd GLIMPSE
make system

Linux (Debian/Ubuntu)

sudo apt install build-essential libboost-iostreams-dev libboost-program-options-dev libboost-serialization-dev libhts-dev libdeflate-dev libbz2-dev liblzma-dev libcurl4-openssl-dev libssl-dev zlib1g-dev
git clone --recursive https://github.com/odelaneau/GLIMPSE.git
cd GLIMPSE
make system

For detailed instructions including building dependencies from source, see the step-by-step guide on the website.

Docker images

Dockerhub

You can find GLIMPSE on docker hub at this link: https://hub.docker.com/r/simrub/glimpse/

Local download from Github releases

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