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Read-based phasing of related individuals
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
Number of Authors: 3
2016 (English)In: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811, Vol. 32, no 12, 234-242 p.Article in journal (Refereed) Published
Abstract [en]

Motivation: Read-based phasing deduces the haplotypes of an individual from sequencing reads that cover multiple variants, while genetic phasing takes only genotypes as input and applies the rules of Mendelian inheritance to infer haplotypes within a pedigree of individuals. Combining both into an approach that uses these two independent sources of information-reads and pedigree-has the potential to deliver results better than each individually. Results: We provide a theoretical framework combining read-based phasing with genetic haplotyping, and describe a fixed-parameter algorithm and its implementation for finding an optimal solution. We show that leveraging reads of related individuals jointly in this way yields more phased variants and at a higher accuracy than when phased separately, both in simulated and real data. Coverages as low as 2 x for each member of a trio yield haplotypes that are as accurate as when analyzed separately at 15 x coverage per individual.

Place, publisher, year, edition, pages
2016. Vol. 32, no 12, 234-242 p.
National Category
Biological Sciences Environmental Biotechnology Computer Science
Identifiers
URN: urn:nbn:se:su:diva-132405DOI: 10.1093/bioinformatics/btw276ISI: 000379734300027OAI: oai:DiVA.org:su-132405DiVA: diva2:952362
Conference
24th Annual Conference on Intelligent Systems for Molecular Biology (ISMB), Orlando, FL, July 08-12, 2016
Available from: 2016-08-12 Created: 2016-08-11 Last updated: 2016-08-12Bibliographically approved

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Martin, Marcel
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