HapTagger: Tag SNP Selection Using Haplotypes

References:

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Huang, Y.-T. and Chao, K.-M., 2008, “A New Framework for the Selection of Tag SNPs by Multimarker Haplotypes” Journal of Biomedical Informatics, 6: 953-961.

We develop a new program called HapTagger for the selection of tag SNPs based on haplotypes instead of on a single SNP. The tag SNPs found by HapTagger form a set of haplotypes completely predictive of the alleles of all untyped SNPs. HapTagger avoids the need of incorporating a linkage disequilibrium statistic and thus significantly improves the computational efficiency. The internal subroutine used by HapTagger (called FastPerfectLD) which can efficiently compute perfect LD and find tag SNPs based on pairwise LD is also available for separate download.

HapTagger:

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HapTagger is implemented in Java. To run this program, you have to first download the Java Development Kit (JDK) from http://java.sun.com. You can compile the Java sources and then run the program.

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Source code: HapTagger.java, MHTagger.java and CycleRemover.java

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Java classes: you can skip the compiling process by running these classes directly.

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Input file format: Each row represents a haplotype and each column is a SNP. Each column is separated by white space. The major allele is denoted as 0 and minor allele as 1, respectively. For example, given three haplotypes with 5 SNPs, the input file may appear as the following example:

1 0 1 0 0
0 1 0 0 0
1 0 0 0 1

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This program requires one input parameter: the path of input file containing haplotypes. For example, if you run HapTagger with input file test.dat, please type the following in the command line.

java HapTagger test.dat
An output file "test.dat.out" containing the predictive haplotypes for each SNP will be generated.

If you encounter any problem, please contact Prof. Kun-Mao Chao.

 

This site was last updated 01/05/09