1. Joel Bader
  2. FAST


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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

Beta.FAST 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) Pleiotropy genome-Wide Association test (PWiS)

Currently these three functions work only in genotype mode; functions based on summary data will be provided in our next release.

Contact : jianan.zhan@jhu.edu, pchanda2@jhmi.edu

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 Beta.FAST

FAST Paper



Program Options

Input File Format

Output File Format

Merging Results of the Methods


Reference haplotypes from 1000G