Clone wiki

FAST / Home

Overview of FAST Links
This page describes in details the various input/output options and input/output files for FAST. FAST is an application for efficiently running several gene based analysis methods simultaneously and efficiently on the same data set. The following methods are implemented using both linear regression (for quantitative traits) and logistic regression (for dichotomous traits):

(1) GWiS
(2) Bimbam
(3) Vegas
(4) MinSNP
(5) MinSNP-Gene
(6) Gates
(7) Single SNP Regression
(8) All the above methods using summary data (single snp regression coefficients and standard errors)

For ease of analysis of genome-wide data, a single chromosome can be run at a time so that all chromosomes can be run in parallel in a computer cluster. If you need to run specific chromosomal regions, see FAQ

FAST 2.4 is an updated beta version of FAST, which added the following functions:

(1) Single SNP Cox proportional hazard model
(2) Gene-based Cox proportional hazard model in GWiS framework
(3) SNP And Pleiotropic PHenotype Organization (SAPPHO), a new tool we developed for detecting pleiotropic associations.

For FAST 2.4, SAPPHO methods could be run in both genotype and summary mode, while Cox models could be run only in genotype mode.

Contact :,

Citation: Chanda P, Huang H, Arking DE, Bader JS (2013) Fast Association Tests for Genes with FAST. PLoS ONE 8(7): e68585. doi:10.1371/journal.pone.0068585 Link
Download FAST

Download FAST.2.4

FAST Paper



Program Options

Input File Format

Output File Format

Merging Results of the Methods


Reference haplotypes from 1000G