About HapSeq
HapSeq is a program for genotyping calling from next generation sequencing data using haplotype information from jumping reads. We developed a Hidden Markov Model (HMM)-based method for genotype calling 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., 2011).
HapSeq Download
Program Manual
Program History
Citation
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@ms.soph.uab.edu Homepage: http://www.soph.uab.edu/ssg/people/zhi |
or |
Kui Zhang, Ph.D. Section on Statistical Genetics Department of Biostatistics University of Alabama at Birmingham Birmingham, AL, 35294 (205) 996-4094 (phone) (205) 975-2540 (fax) Email: kzhang@ms.soph.uab.edu Homepage: http://www.soph.uab.edu/ssg/zhang |