Welcome users of Fast ASsociation Testing (FAST)

Overview

This documents 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):

GWiS (Huang et. al. PLoS Genet, 7(7):e1002177, Jul 2011)
Bimbam (Servin et. al. PLoS Genet, 3(7):e114, Jul 2007)
Vegas (Lui et. al. Am J Hum Genet, 87(1):139–145, Jul 2010)
MinSNP (Huang et. al. PLoS Genet, 7(7):e1002177, Jul 2011)
MinSNP-Gene (Huang et. al. PLoS Genet, 7(7):e1002177, Jul 2011)
Gates (Am J Hum Genet, 88(3):283–293, Mar 2011)
Single SNP Regression.
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.

Availability

FAST is downloadable from https://bitbucket.org/baderlab/fast/downloads/. Additional files needed for running the software in “summary” mode (haplotypes from a background population see options below) are also available at the same location.

Installation

GNU Scientific Library (GSL) is required to compile and use FAST. GSL can be downloaded from http://www.gnu.org/software/gsl/. After you download GSL, please refer to the INSTALL file within GSL directory for installation of GSL. Once GSL is installed, download FAST and decompress the archive. Go to the software directory and type “make clean” and then type “make”. This should compile the code to produce a binary for the appropriate platform. Next run : ./install.sh . The final executable is named FAST. Type “./FAST --help” to see all the options.

Quickstart scripts

Below are some scripts for quickly getting into analysis using FAST with some standard options. However, before running these, make sure the input file formats are correct.

Quickstart

Runtime Options

FAST Runtime options

Input File Formats

Output File Formats

Preparing an Integrated Report

Integrated Report

Examples

Wiki

FAST / OldHome