HapSeq

HapSeq2 - A Program for Haplotype Phasing and Genotype Calling from Next Generation Sequencing Data

Using Haplotype Information of Jumping Reads

Degui Zhi and Kui Zhang

About HapSeq2

HapSeq2 is a program for genotyping calling and haplotype phasing from next generation sequencing data using haplotype information from jumping reads. Previously, 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 (Zhi et al., 2012). The method is implemented in the program, HapSeq. The program is written with C++ and based on the source code of Thunder program provided by Drs. Yun Li and Goncalo Abecasis. The detailed description of the method implemented in HapSeq can be found in our manuscript (Zhi et al., 2012).

Recently, we extended our methods to incorporate the haplotype information of multiple adjacent and/or non-adjacent sites from sequencing reads. Our model is inspired by the model implemented in HASH that was originally designed to phase individual genomes (Bansal et al., 2008). We develop a new hybrid MCMC algorithm that combines the Gibbs sampling algorithm of HapSeq and Metropolis-Hasting algorithm similar to that of HASH and is computationally feasible. We show by simulation and real data from the 1000 Genomes Project that our model offers superior performance for haplotype phasing as well as genotype calling for population NGS data over existing methods. The new method is implemented in the program, HapSeq2. For the detailed description of the method implemented in HapSeq2, please refer to our manuscripts (Zhi et al., 2012; Zhang and Zhi, 2013).

HapSeq2 Download

• • HapSeq2.zip. This file includes the complied program of HapSeq2 with the Window XP and Linux operating systems, the program manual and the example with corresponding input files.

Program Manual

• • HapSeq2 Manual

Input Files

• • A set of input files are needed for HapSeq2. Please refer to HapSeq2 Manual for the detailed description of these input files. In general, these files should be extracted from a set of read alignment (BAM) files. We have implemented several programs to extract the input files required by HapSeq2. The programs and the pipeline to use these programs are described at this Wiki Page.

Old Program

• • Please go to this Web Site to find and download the old version of HapSeq.

Program History

• • December 15, 2011: The program HapSeq is implemented and released.

  • January 4, 2013: The program HapSeq2 is implemented and released.

References

• • Bansal V, Halpern AL, Axelord N, Bafna V. 2008. An MCMC algorithm for haplotype assembly from whole-genome sequence data. Genome Research 18: 1336-1346.

  • 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.

  • Zhang K, Zhi D. 2013. Joint haplotype phasing and genotype calling of multiple individ-uals using long-range haplotype informative reads. Submitted to Bioinformatics.

How to Cite

Please cite the following papers if you use our program:

• • 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.

  • Zhang K, Zhi D. 2013. Joint haplotype phasing and genotype calling of multiple individuals using long-range haplotype informative reads. Submitted to Bioinformatics.

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:

Created Date: Jan 4, 2013

Last Updated Date: Sep 17, 2015