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WhatsHap: fast and accurate read-based phasing

View ORCID ProfileMarcel Martin, View ORCID ProfileMurray Patterson, Shilpa Garg, Sarah O Fischer, View ORCID ProfileNadia Pisanti, View ORCID ProfileGunnar W Klau, Alexander Schöenhuth, View ORCID ProfileTobias Marschall
doi: https://doi.org/10.1101/085050
Marcel Martin
1Science for Life Laboratory, Dept of Biochemistry and Biophysics, Stockholm University, Box 1031, SE-17121 Solna, Sweden.
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Murray Patterson
2Experimental Algorithmics Lab (AlgoLab), Dipartimento di Informatica Sistemistica e Comunicazione (DISCo), Università degli Studi di Milano-Bicocca, 20126, Milano, Italy.
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Shilpa Garg
3Center for Bioinformatics, Saarland University, Saarland Informatics Campus E2.1, 66123, Saarbrücken, Germany.
4Max Planck Institute for Informatics, Saarland Informatics Campus E1.4, Saarbrücken, Germany.
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Sarah O Fischer
3Center for Bioinformatics, Saarland University, Saarland Informatics Campus E2.1, 66123, Saarbrücken, Germany.
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Nadia Pisanti
5Department of Computer Science, University of Pisa, Italy.
6Erable Team, INRIA Grenoble Rhône-Alpes, 655 Avenue de l'Europe, 38330, Montbonnot Saint-Martin, France.
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Gunnar W Klau
7Life Sciences Group, Centrum Wiskunde & Informatica (CWI), Science Park 123 1098 XG Amsterdam, The Netherlands.
6Erable Team, INRIA Grenoble Rhône-Alpes, 655 Avenue de l'Europe, 38330, Montbonnot Saint-Martin, France.
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Alexander Schöenhuth
7Life Sciences Group, Centrum Wiskunde & Informatica (CWI), Science Park 123 1098 XG Amsterdam, The Netherlands.
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Tobias Marschall
3Center for Bioinformatics, Saarland University, Saarland Informatics Campus E2.1, 66123, Saarbrücken, Germany.
4Max Planck Institute for Informatics, Saarland Informatics Campus E1.4, Saarbrücken, Germany.
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  • For correspondence: t.marschall@mpi-inf.mpg.de
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Abstract

Read-based phasing allows to reconstruct the haplotypes of a sample purely from sequencing reads. While phasing is an important step for answering questions about population genetics, compound heterozygosity, and to aid in clinical decision making, there has been a lack of accurate, usable and standards-based software.

WhatsHap is a production-ready tool for highly accurate read-based phasing. It was designed from the beginning to leverage third-generation sequencing technologies, whose long reads can span many variants and are therefore ideal for phasing. WhatsHap works also well with second-generation data, is easy to use and will phase not only SNVs, but also indels and other variants. It is unique in its ability to combine read-based with pedigree-based phasing, allowing to further improve accuracy if multiple related samples are provided.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted November 14, 2016.
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WhatsHap: fast and accurate read-based phasing
Marcel Martin, Murray Patterson, Shilpa Garg, Sarah O Fischer, Nadia Pisanti, Gunnar W Klau, Alexander Schöenhuth, Tobias Marschall
bioRxiv 085050; doi: https://doi.org/10.1101/085050
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WhatsHap: fast and accurate read-based phasing
Marcel Martin, Murray Patterson, Shilpa Garg, Sarah O Fischer, Nadia Pisanti, Gunnar W Klau, Alexander Schöenhuth, Tobias Marschall
bioRxiv 085050; doi: https://doi.org/10.1101/085050

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