Single Marker Association 2.0

Single Marker Association is a simple tool that calculates the single marker association between individual SNP markers.

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LICENSE TYPE:
GPL (GNU General Public License) 
USER RATING:
2.4/5 14
DEVELOPED BY:
Thomas Mailund
HOMEPAGE:
www.daimi.au.dk
CATEGORY:
ROOT \ Science and Engineering \ Bioinformatics
Single Marker Association is a simple tool that calculates the single marker association between individual SNP markers and a case/control dichotomy.

Usage:

The tool reads two files as input, the first is a set of case and the second a case of control haplotypes. The format of the files is one line per haplotype, where the SNP data is represented as 0 or 1, separated by white-space.

· The tool outputs a list of statistics for each marker
· The marker number (from left to right in the input data)
· The frequency of the 0 allele for the cases file
· The chi-square contingency table statistics for the marker
· The CDF of the chi-square statistics
· The p-value of the statistics (1-CDF)

Installation:

The SMA tool is written in C++. It should compile on any Unix like system. To install, download the source code and unpack it (tar xzf sma-v.tar.gz, where v is the version number of sma), then run make in the subdirectory sma-v created during unpacking.

What's New in This Release:

· Support for (unphased) genotype data.

Last updated on January 19th, 2006

#marker association #SNP markers #control dichotomy #marker #association #SNP #dichotomy

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