Table 1.
Useful software packages for data management, quality control, and statistical analysis in genome-wide association studies.
| Software package |
URL | Purpose |
|---|---|---|
| PLINK | http://pngu.mgh.harvard.edu/~purcell/plink/ | Free, open-source GWAS analysis software package. Contains many tools for data management, quality control, and statistical analysis. (PC, Mac, Linux). |
| PLATO | https://chgr.mc.vanderbilt.edu/plato |
PLatform for the Analysis, Translation, and Organization of large-scale data – software for GWAS analysis similar to PLINK. |
| R | http://www.r-project.org/ | Free, open-source statistical computing software with excellent graphical capabilities. (PC, Mac, Linux). |
| Eigensoft | http://genepath.med.harvard.edu/~reich/Software.htm | Free, open-source software for performing principal components analysis based method for detecting and correcting for population stratification in GWAS. (Linux only). |
| Structure | http://pritch.bsd.uchicago.edu/structure.html | Free, open-source software for inferring the presence of distinct populations and assigning individuals to those populations for a stratified analysis. (Windows, Mac, Linux) |
| MySQL Workbench |
http://wb.mysql.com/ | Free, open-source software for creating, administering and querying relational databases. This is helpful for subsetting data, merging results, and joining QC metrics (e.g. HWE) to final association results. (Windows, Mac, Linux). |