Single Marker Association

Single Marker Association is a software tool designed for calculating the single marker association between individual SNP markers and a case/control dichotomy. This tool can be used to output a list of statistics for each marker, including 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, and the p-value of the statistics (1-CDF).

To use the Single Marker Association tool, two files are required as input: the first file is a set of case haplotypes and the second file is a set of control haplotypes. The format of the files should be one line per haplotype, where the SNP data is represented as 0 or 1 and separated by white-space.

The installation process for SMA is straightforward. The tool is written in C++ and should compile on Unix-like systems. To install SMA, simply download the source code and unpack it using the command "tar xzf sma-v.tar.gz," where "v" is the version number of sma. Once unpacked, run "make" in the subdirectory sma-v created during unpacking.

The latest release of the Single Marker Association tool includes support for (unphased) genotype data. Overall, this software tool is a simple yet effective way to calculate the single marker association between individual SNP markers and a case/control dichotomy.