HapSeq - A Program for Genotype Calling and Phasing from Next Generation Sequencing Data
Using Haplotype Information of Jumping Reads
Degui Zhi, Jihua Wu, Nianjun Liu, Kui Zhang
About HapSeq
HapSeq is a program for genotyping calling and haplotype phasing from next generation sequencing data using haplotype information from jumping reads. We developed a Hidden Markov Model (HMM)-based method for genotype calling and haplotype phasing from next generation data that can take into account jumping reads information across two adjacent potential polymorphic sites. Our method extends the HMM in the Thunder program (Li, et al., 2010) and explicitly models jumping reads information as emission probabilities conditional on the states of adjacent sites. The method is implemented in the program, HapSeq. The program is implemented with C++ and based on the source code of Thunder program provided by Drs. Yun Li and Goncalo Abecasis. For the detailed description of the method implemented in HapSeq, please refer to our manuscript (Zhi et al., 2012).
HapSeq Download
HapSeq.zip. This file includes the complied program of HapSeq with the Window XP and Linux operating systems, the program manual, the examples, and two perl scripts that can generate the input files required by HapSeq from a set of read alignment (BAM) files.
Program Manual
HapSeq Manual
Program History
December 15, 2011: the program is implemented and released.
Citation
Li Y, Willer CJ, Scheet P, Abecasis GR. 2010. MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes. Genetic Epidemiology 34: 816-834.
Zhi D, Wu J, Liu N, Zhang K. 2012. Genotype calling from next-generation sequencing data using haplotype information of reads. Bioinformatics 28: 938-946.
We are planning to update our program regularly. You are welcome to suggest features that you want us to implement into this program. We greatly appreciate if you could point out any bugs when you use our program. Our contact information is:
Degui Zhi, Ph.D.
Section on Statistical Genetics
Department of Biostatistics
University of Alabama at Birmingham
Birmingham, AL, 35294
(205) 975-9192 (phone)
(205) 975-2540 (fax)
Email: dzhi@uab.edu
Homepage: http://www.soph.uab.edu/ssg/people/zhi
or
Kui Zhang, Ph.D.
Department of Mathematical Sciences
Michigan Technological University
1400 Townsend Drive
Houghton, Michigan 49931
Phone: 906-487-2918
Fax: 906-487-3133
Email: kuiz@mtu.edu
Created Date: Dec 15, 2011
Last Updated Date: Sep 17, 2015