Publication Details
Title: Haplotype Reconstruction Using Perfect Phylogeny and Sequence Data
Author: A. Efros and E. Halperin
Group: Algorithms
Date: April 2012
PDF: http://www.icsi.berkeley.edu/pubs/algorithms/ICSI_haplotypereconstruction12.pdf
Overview:
Haplotype phasing is a well studied problem in the context of genotype data. With the recent developments in high-throughput sequencing, new algorithms are needed for haplotype phasing, when the number of samples sequenced is low and when the sequencing coverage is blow. High-throughput sequencing technologies enables new possibilities for the inference of haplotypes. Since each read is originated from a single chromosome, all the variant sites it covers must derive from the same haplotype. Moreover, the sequencing process yields much higher SNP density than previous methods, resulting in a higher correlation between neighboring SNPs. We offer a new approach for haplotype phasing, which leverages on these two properties. Our suggested algorithm, called Perfect Phlogeny Haplotypes from Sequencing (PPHS) uses a perfect phylogeny model and it models the sequencing errors explicitly. We evaluated our method on real and simulated data, and we demonstrate that the algorithm outperforms previous methods when the sequencing error rate is high or when coverage is low.
Bibliographic Information:
Proceedings of the Second Annual Satellite Workshop on Massively Parallel Sequencing at the 16th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2012), Barcelona, Spain. Published in BMC Bioinformatics, Vol. 13, Suppl. 6:S2
Bibliographic Reference:
A. Efros and E. Halperin. Haplotype Reconstruction Using Perfect Phylogeny and Sequence Data. Proceedings of the Second Annual Satellite Workshop on Massively Parallel Sequencing at the 16th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2012), Barcelona, Spain. Published in BMC Bioinformatics, Vol. 13, Suppl. 6:S2, April 2012
Author: A. Efros and E. Halperin
Group: Algorithms
Date: April 2012
PDF: http://www.icsi.berkeley.edu/pubs/algorithms/ICSI_haplotypereconstruction12.pdf
Overview:
Haplotype phasing is a well studied problem in the context of genotype data. With the recent developments in high-throughput sequencing, new algorithms are needed for haplotype phasing, when the number of samples sequenced is low and when the sequencing coverage is blow. High-throughput sequencing technologies enables new possibilities for the inference of haplotypes. Since each read is originated from a single chromosome, all the variant sites it covers must derive from the same haplotype. Moreover, the sequencing process yields much higher SNP density than previous methods, resulting in a higher correlation between neighboring SNPs. We offer a new approach for haplotype phasing, which leverages on these two properties. Our suggested algorithm, called Perfect Phlogeny Haplotypes from Sequencing (PPHS) uses a perfect phylogeny model and it models the sequencing errors explicitly. We evaluated our method on real and simulated data, and we demonstrate that the algorithm outperforms previous methods when the sequencing error rate is high or when coverage is low.
Bibliographic Information:
Proceedings of the Second Annual Satellite Workshop on Massively Parallel Sequencing at the 16th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2012), Barcelona, Spain. Published in BMC Bioinformatics, Vol. 13, Suppl. 6:S2
Bibliographic Reference:
A. Efros and E. Halperin. Haplotype Reconstruction Using Perfect Phylogeny and Sequence Data. Proceedings of the Second Annual Satellite Workshop on Massively Parallel Sequencing at the 16th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2012), Barcelona, Spain. Published in BMC Bioinformatics, Vol. 13, Suppl. 6:S2, April 2012