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 was developed at Harvard Genetics Department and the Broad Institute.How to run
The environment variable(s) need to be set properly first. The easiest way to do this is by using the modules commands as in the example below.
[user@helix]$ module avail eigensoft ----------------------------- /usr/local/Modules/3.2.9/modulefiles -------------------------- eigensoft/2.0 eigensoft/3.0 eigensoft/4.2(defaul [user@helix]$ module load eigensoft [user@helix]$ module list Currently Loaded Modulefiles:
1) eigensoft/4.2 [user@helix]$ module unload eigensoft [user@helix]$ module load eigensoft/3.0 [user@helix]$ module list Currently Loaded Modulefiles: 1) eigensoft/3.0 [user@helix]$ module show eigensoft ------------------------------------------------------------------- /usr/local/Modules/3.2.9/modulefiles/eigensoft/4.2: module-whatis Sets up eigensoft 4.2 prepend-path PATH /usr/local/apps/eigensoft/4.2/bin -------------------------------------------------------------------
$ module load eigensoft $ 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
http://helix.nih.gov/Applications/README.eigensoft
http://helix.nih.gov/Applications/README.eigenstrat
http://helix.nih.gov/Applications/README.popgen
http://helix.nih.gov/Applications/README.convertf
