gigi2

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 genotypes.
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'