PRESTO: Genetic Association Analysis Software
Program: PRESTO
Version: 1.0.1
Copyright (c) 2007-8 Brian L. Browning
Email: b.browning@auckland.ac.nz
This page was last updated on 20 June 2008
All rights reserved
Contents
Introduction
PRESTO is optimized software for permutation testing and for computing empirical distributions
of order statistics via permutation. PRESTO is extremely fast and can efficiently
analyze data from one and two-stage whole genome association studies with millions of markers genotyped
on thousands of samples. PRESTO can
- perform allelic and genotypic tests of marker data and a binary trait
- analyze stratified data
- analyze combined single-marker and haplotypic cluster data produced using the
BEAGLE software package.
.
- determine multiple-testing adjusted p-values
- compute empirical distributions of order statistics to determine the
statistical significance for sets of top-ranked markers.
- determine significance levels to control type 1 error for
one and two-stage genotyping designs
- run in parallel using multiple computer processors
PRESTO is written in Java and runs on most computing platforms (e.g. Windows, Linux,
Unix, Solaris, Mac).
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Citation
If you use PRESTO in a published analysis, please cite
B L Browning. PRESTO: Rapid calculation of order statistic distributions and multiple-testing adjusted p-values via permutation for one and two-stage genetic association studies [Abstract 2045]. Presented at the annual meeting of The American Society of Human Genetics, October 23-27, 2007, San Diego, CA. Available from
http://www.ashg.org.
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Download PRESTO 1.0.1
PRESTO is a software program genetic association analysis. Because PRESTO (the program)
is licensed free of charge, there is NO WARRANTY for the program, to the extent
permitted by applicable law. Brian Browning (the copyright holder) and/or other
parties provide the program "as is" without warranty of any kind, either expressed
or implied, including, but not limited to, the implied warranties of merchantability
and fitness for a particular purpose. The entire risk as to the quality and performance
of the program is with you. Should the program prove defective, you assume the cost of
all necessary servicing, repair or correction.
In no event unless required by applicable law or agreed to in writing will any copyright
holder be liable to you for damages, including any general, special, incidental or consequential
damages arising out of the use or inability to use the program (including but not limited to
loss of data or data being rendered inaccurate or losses sustained by you or third parties
or a failure of the program to operate with any other programs), even if such holder or other
party has been advised of the possibility of such damages.
The PRESTO 1.0.1 software distribution includes the following files:
- presto_1.0.pdf: The documentation for PRESTO 1.0
- presto.jar: The executable file for running PRESTO
- example: A folder containing 1 input file and 3 output files
from an analysis described in the PRESTO 1.0 documentation.
- utility: A folder containing a utility program for formatting
input files for PRESTO analysis.
The utility program is described in the PRESTO 1.0 documentation
Source code for PRESTO will be made available as soon as a brief report describing PRESTO is published.
Brian Browning grants you permission to use PRESTO version 1.0.1
for research purposes. If you understand
PRESTO is distributed without warranty, and would like to download PRESTO
click here.
To download a short R script for creating QQ-plots, click here
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Version History
- Version 1.0.1 (10 Oct 2007): First public release of PRESTO
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