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WinHAP 1.0

Phasing Software Package


WinHAP1.0 is a fast haplotype phasing program based on scalable sliding windows. It allows a rapid and more accurate inference of haplotype from population genotype data. WinHAP1.0 generates a initial haplotypes set in first step, using a simplified process of 2SNP algorithm. Then scalable sliding windows are used to correct the initial haplotypes. At last, the phasing solution is further optimized by using a new greedy technology based on parsimony principle. It outperforms most of the existing algorithms in terms of both speed and accuracy.


The software WinHAP1.0 is free for non-commercial use. Linux and Windows executables are available for download:

If the buttons do not work, you can send an e-mail to the authors which includes:

subject: Request for WinHAP Package
1. Name.
2. Affiliation.
3. Version of operating system.
4. Maximum datasize (# of genotypes in your data / # of SNPs in your data).

Program Usage

You can run the executables directly as follow:

      winhap [GenotypesFileName] [HaplotypesFileName] [-i iterations]

If you can't remember the parametres of the program, you can get help by running "winhap --help". The program can also be run using the default parameters as follows:

      winhap genotypes.in haplotypes.out

If you want using the default parameters, you must guarantee the file of genotypes.in is existing, and the file is not empty. The value of iterations is the number which sets the account of the program decreasing the result haplotypes iteratively.

InputFile formats:

    One line per genotype, SNPs values are in {0,1,2,?}
    0 - homozygous SNP with major allele
    1 - homozygous SNP with minor allele
    2 - heterozygous SNP
    ? - missing data

OutputFile formats:

Two haplotypes per genotype.

    One line per haplotype, SNPs values are in {0,1}
    0 - major allele SNP
    1 - minor allele SNP

Sample input and output:

    The input file genotypes.in contains 9 genotypes each with 96 SNPs.

    The output file haplotypes.out is a result phased by WinHAP for genotypes.in, which contains 18 haplotypes each with 96 SNPs.


    The number of genotypes should not more than 1000, and the length of per genotype should not more than 10000 for the version 1.0.


If you use WinHAP in public, please report the WinHAP version used and cite the publication:
    · Xu Y, Cheng WH, Nie PY, Zhou FF (2012) WinHAP: an Efficient Haplotype Phasing Algorithm based on Scalable Sliding Windows ..


Wenhua Cheng
Phone: +8618725515363
Email: cwh@mail.ustc.edu.cn
Office: 502, NHPCC(Hefei), USTC, Jinzhai Road
Homepage: http://staff.ustc.edu.cn/~xuyun/winhap/WHCheng.htm

Yun Xu
Phone: +86-551-3602441
Email: xuyun@ustc.edu.cn
Homepage: http://staff.ustc.edu.cn/~xuyun/

Since December 15, 2011. Updated December 17, 2011


I wish to thank Haiyang Tu and Chunlei Yan for providing many helps to me.