shapeit

SHAPEIT is a fast and accurate method for estimation of haplotypes (aka phasing) from genotype or sequencing data.

• Version: 2.904
• Added: July, 2023
• Link: https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html

See which versions are available:

$ module avail shapeit

Load one version into your environment and run it:

$ module load shapeit/2.904
$ shapeit --help

Notes from the sysadmin during installation:

$ cd /tmp
$ wget https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.v2.r904.glibcv2.17.linux.tar.gz
$ sudo mkdir -p /export/apps/shapeit/2.904
$ sudo cp -r shapeit.v2.904.3.10.0-693.11.6.el7.x86_64/* /export/apps/shapeit/2.904