smartpca

reduction of population bias for genetic analyses

Install

All systems
curl cmd.cat/smartpca.sh
Debian Debian
apt-get install eigensoft
Ubuntu
apt-get install eigensoft
image/svg+xml Kali Linux
apt-get install eigensoft
Raspbian
apt-get install eigensoft

eigensoft

reduction of population bias for genetic analyses

The EIGENSOFT package combines functionality from the group's population genetics methods (Patterson et al. 2006) and their EIGENSTRAT stratification method (Price et al. 2006). The EIGENSTRAT method uses principal components analysis to explicitly model ancestry differences between cases and controls along continuous axes of variation; the resulting correction is specific to a candidate marker's variation in frequency across ancestral populations, minimizing spurious associations while maximizing power to detect true associations. The EIGENSOFT package has a built-in plotting script and supports multiple file formats and quantitative phenotypes.