Software

EIGENSOFT

(April 2014): EIGENSOFT version 5.0.2 is now available for download. The EIGENSOFT package combines functionality from our population genetics methods (Patterson et al. 2006) and our EIGENSTRAT stratification correction 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.

Source code, documentation and executables for using EIGENSOFT 5.0.2 on a Linux platform can be downloaded here. New features of EIGENSOFT 5.0 include expanded options for LD regression in computing the GRM, a new option for outputting the GRM (compatible with GCTA software), a new option for PCA projection with large amounts of missing data, and a bug fix for PLINK format files with out-of-order SNPs.  EIG5.0.2 incorporates a minor bug fix in the input/output library.  EIGENSOFT 5.0 does not support multi-threading.  Users who wish to use multi-threading should use EIGENSOFT 4.2, which can be downloaded here.

The EIGENSOFT FAQ (Frequently Asked Questions) is available here. For further questions about the EIGENSOFT software, please write to Samuela Pollack (spollack@hsph.harvard.edu).

SOFTWARE REGISTRATION: we encourage EIGENSOFT users to register here. Registration is voluntary, but will allow us to send information about software updates.

HAPMIX

(March 2011): HAPMIX version 1.2 can be downloaded here. Improvements to version 1.2 include an explicit check for discordance between admixed and reference population allele frequencies, and a script to interpolate estimates of local ancestry to a superset of SNPs. HAPMIX is an application for accurately inferring chromosomal segments of distinct continental ancestry in admixed populations, using dense genetic data.For details, see the HAPMIX paper (Price et al. 2009).

MIXSCORE

(July 2012): MIXSCORE version 1.3 can be downloaded here. MIXSCORE is a method for combining SNP association and admixture association statistics to increase power in GWAS in admixed populations. For details, see the MIXSCORE paper (Pasaniuc et al. 2011 PLoS Genet, “Enhanced statistical tests for GWAS in admixed populations: assessment using African Americans from CARe and a breast cancer consortium”).

LTSOFT

(June 2013): LTSOFT version 2.0 can be downloaded here. Changes to version 2.0 include consolidation of the code for fitting clinical covariate and genetic covariate parameters into a single program (ltfit) and a bugfix to the code for fitting genetic covariate parameters. LTSOFT is a software suite designed to more powerfully leverage clinical-covariates such as age, bmi, smoking status, and gender as well as genetic-covariates such as known associated variants when conducting case-control association studies. Including these covariates in standard regression models is not only suboptimal, but can in many instances reduce power. LTSOFT employs a liability threshold model approach that takes advantage of known epidemiological results to better model the covariates’ relationship to the phenotype of interest (Zaitlen et al. 2012 PLoS Genet and Zaitlen et al. 2012 Bioinformatics).

TREESELECT

(April 2012): TreeSelect version 1.1 can be downloaded here. TreeSelect is a software package for inferring natural selection from unusual population differentiation between closely related populations. For details, see our Africa selection paper (Bhatia et al. 2011 AJHG, “Genome-wide comparison of African-ancestry populations from CARe and other cohorts reveals signals of natural selection.”)

GENE EXPRESSION HERITABILITY

(January 2011): Source code and gene-by-gene results from our gene expression heritability paper “Single-tissue and cross-tissue heritability of gene expression via identity-by-descent in related or unrelated individuals” (Price et al. 2011) can be downloaded here.

SNPWEIGHTS

(May 2014): SNPweights version 2.1 can be downloaded here.  SNPweights is a software package for inferring genome-wide genetic ancestry using SNP weights precomputed from large external reference panels (Chen et al. 2013 Bioinformatics).  Changes to version 2.0 include new SNP weights for Native American reference samples, a new format for SNP weights files, and new software for users to derive SNP weights using their own reference samples.  Version 2.1 incorporates a bug fix in the inferanc program, which now works with all snpwt files.  SNP weights for European and West African ancestral populations can be downloaded here. SNP weights for European, West African and East Asian ancestral populations can be downloaded here. SNP weights for European, West African, East Asian and Native American ancestral populations can be downloaded here.  SNP weights for NW, SE and AJ ancestral populations of European Americans can be downloaded here.

IMPG-SUMMARY

(July 2013):  ImpG-Summary version 1.0 can be downloaded here.  ImpG-Summary is a software package for Gaussian imputation from summary association statistics, as described in our paper “Fast and accurate imputation from summary association statistics” (Pasaniuc et al., submitted).

FUNCTIONAL ANNOTATIONS

(March 2014): Functional annotations of SNPs and regions from our functional heritability paper “Regulatory variants explain much more heritability than coding variants across 11 common diseases” (Gusev et al., submitted) can be downloaded here.