WhatsHap: fast and accurate read-based phasing
By Marcel Martin, Murray Patterson, Shilpa Garg, Sarah O Fischer, Nadia Pisanti, Gunnar W. Klau, Alexander Schöenhuth, Tobias Marschall. bioRxiv, 2016
406 citations recorded by the source corpus.
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.
Subfields: Genetics
View Paper: https://www.semanticscholar.org/paper/4acd0eb336db09bed221448e5d8be0ad8b04dbc0
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In Genetics
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Citations in the corpus
- Haplotype-resolved diverse human genomes and integrated analysis of structural variation (2021, background): “StrandphaseR ( 70 ), SaaRclust ( 71 ), and WhatsHap ( 72 , 73 ) partitioned long reads into haplotypes to generate phased genome assemblies ( 3 ).”