Read-Based Phasing and Analysis of Phased Variants with WhatsHap

Marcel Martin; Peter Ebert; Tobias Marschall

doi:10.1007/978-1-0716-2819-5_8

Read-Based Phasing and Analysis of Phased Variants with WhatsHap

Methods Mol Biol. 2023:2590:127-138. doi: 10.1007/978-1-0716-2819-5_8.

Authors

Marcel Martin¹, Peter Ebert², Tobias Marschall³

Affiliations

¹ Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Solna, Sweden. marcel.martin@scilifelab.se.
² Institute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany. peter.ebert@iscb.org.
³ Institute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany. tobias.marschall@hhu.de.

PMID: 36335496
DOI: 10.1007/978-1-0716-2819-5_8

Abstract

WhatsHap is a command-line tool for phasing and phasing-related tasks. It allows to infer haplotypes in diploid and polyploid samples based on (preferably long) reads covering at least two heterozygous variants. It offers additional tools for working with phased variant calls such as computing statistics, comparing different phasings and assigning reads in alignment files to their haplotype.

Keywords: Haplotype assembly; Long reads; Pedigree phasing; Polyploid phasing; Read-based phasing.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Algorithms
Diploidy*
Haplotypes / genetics
Heterozygote
Humans
Polymorphism, Single Nucleotide
Polyploidy*
Sequence Analysis, DNA