GIGI2 is a computer program to impute missing genotypes on pedigrees. The
approach handles large pedigrees by using a Markov Chain Monte Carlo-based
program to infer inheritance vectors. Our approach has 2 steps: 1. use the
program gl_auto from the MORGAN package to infer inference vectors using
genotypes from informative framework markers 2. use GIGI to impute missing
Note 1: gl_auto and MORGAN are NOT included in this snap, gl_auto
should be obtained through its own channels. GIGI2 inputs are outputs from gl_auto.
Note 2: The strict confinement of this app limits where it can write to. To allow it to write in your home directory, you need to attach the home interface to the snap. Likewise if you need to write to external devices mounted in /mnt or /media.
e.g. 'snap connect gigi2:home :home' to be able to write in your /home/user
and 'snap connect gigi2:removable-media :removable-media' to write in
/mnt/vol_name and /media/vol_name
If you need to write to other locations, then you will need to install the
snap in devmode, e.g. 'snap install --devmode gigi2' If it was already
installed and you need to install in devmode, then I recommend first
removing the currently installed version, 'snap remove gigi2'
For versions of Ubuntu between 14.04 LTS (Trusty Tahr) and 15.10 (Wily Werewolf), as well as Ubuntu flavours that don’t include snap by default, snap can be installed from the Ubuntu Software Centre by searching for snapd.
Alternatively, snapd can be installed from the command line:
sudo apt update
sudo apt install snapd
Either log out and back in again, or restart your system, to ensure snap’s paths are updated correctly.
To install gigi2, simply use the following command: