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bioRxiv · 10.1101/085050

WhatsHap: fast and accurate read-based phasing

Martin, M.·Patterson, M.·Garg, S.·Fischer, S.·Pisanti, N.·Klau, G. W.·Schoenhuth, A.·Marschall, T.
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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.\n\nWhatsHap 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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Martin, M., Patterson, M., Garg, S., Fischer, S., Pisanti, N., Klau, G. W., Schoenhuth, A., Marschall, T.. 2016-11-02. WhatsHap: fast and accurate read-based phasing. https://doi.org/10.1101/085050

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