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: including 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 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 parameters: the path of input file containing haplotypes. For example,
if you run HapTagger with input file test.dat. In the command line, please type
java HapTagger test.dat
An output file "test.dat.out"
containing the predictive haplotypes for each SNP will be generated.
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If you encounter any problem, please contact Prof. Kun-Mao Chao.
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