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Read-Based Phasing and Analysis of Phased Variants with WhatsHap
Marcel Martin1, Peter Ebert2, Tobias Marschall3
1Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Solna, Sweden. marcel.martin@scilifelab.se.
Methods in Molecular Biology (Clifton, N.J.)
|November 6, 2022
Summary
WhatsHap is a command-line tool that infers haplotypes from sequencing reads in diploid and polyploid samples. It also provides utilities for analyzing and comparing haplotype phasing results.
Area of Science:
- Genomics
- Bioinformatics
Background:
- Haplotype phasing is crucial for understanding genetic variation and inheritance patterns.
- Accurate haplotype inference is essential for various genomic analyses, including population genetics and clinical applications.
Purpose of the Study:
- To introduce WhatsHap, a versatile command-line tool for haplotype phasing and related tasks.
- To provide a comprehensive solution for inferring and analyzing haplotypes from sequencing data.
Main Methods:
- WhatsHap utilizes sequencing reads, preferably long reads, that cover at least two heterozygous variants.
- The tool supports phasing in both diploid and polyploid organisms.
- It incorporates additional functionalities for statistical analysis, comparison of phasing outcomes, and read assignment to specific haplotypes.
Main Results:
- WhatsHap successfully infers haplotypes in diverse sample types.
- The tool facilitates downstream analyses of phased variant calls, enhancing the utility of genomic data.
- Additional utilities enable robust evaluation and management of phasing results.
Conclusions:
- WhatsHap offers an efficient and comprehensive solution for haplotype phasing.
- The tool's versatility makes it valuable for researchers in genomics and bioinformatics.
- WhatsHap supports advanced analysis of phased genomic data.
