Description

The EIGENSOFT package combines functionality from population genetics methods (Patterson et al. 2006) and EIGENSTRAT stratification correction me thod (Price et al. 2006). The EIGENSTRAT method uses principal components analysis to explicitly model ancestry differences between cases and controls along continuous axe s 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.

Eigensoft is intended to be run interactively on Helix.

Version

view file /usr/local/eigensoft/README

How to run an interactive job

Create a directory for the job and put all the required input files in the directory. There are sample files under /usr/local/eigensoft/EIGENSTRAT/. User can copy them into the directory just created.

Add to your path /usr/local/eigensoft/bin. This directory contains all executables in the package.

For csh or tcsh users, issue this command: % set path=( /usr/local/eigensoft/bin ${path} )
For bash/ksh/sh users, issue this command: % PATH=/usr/local/eigensoft/bin:$PATH

Start running the programs. For example:

% smartpca.perl -i example.geno -a example.snp -b example.ind -k 5 \
-o example.pca -p example.plot -e example.eval -l example.log -m maxiter \
-t topk -s sigma
% eigenstrat -i example.geno -j example.pheno -p example.pca -l 1 \
-o example.chisq
% gc.perl example.chisq example.chisq.out

Documentation

/usr/local/eigensoft/README
/usr/local/eigensoft/EIGENSTRAT/README
/usr/local/eigensoft/POPGEN/README
/usr/local/eigensoft/CONVERTF/README