ArticleBioinformatics (Oxford, England)2016
Read-based phasing of related individuals.
Article in Bioinformatics (Oxford, England), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- The rate and spectrum of germline mutations in chicken from a commercial pedigree line.Genetics, selection, evolution : GSE · 2026Article
- Long-read genome sequencing improves detection and functional interpretation of structural and repeat variants in autism.Cell genomics · 2026Article
- Determinants of haplotype phasing accuracy in long-read human genome sequencing.bioRxiv : the preprint server for biology · 2026Article
- Characterization of de novo germline mutations suggests a strong male mutation bias in coppery titi monkeys (Plecturocebus cupreus).Molecular biology and evolution · 2026Article
- Benchmarking imputation accuracy in the presence or absence of a reference panel.Molecular biology and evolution · 2026Article
- Evolution and Comparative Analysis of Sheep Reference Genomes: From Fragmented Assemblies to Telomere-to-Telomere Genomics.Biology · 2026Review
- Genomic imprinting at a porcine ZNF locus via a canonical imprinting mechanism.Animal genetics · 2025Article
- Parameterizing Pantherinae: De Novo Mutation Rate Estimates from Panthera and Neofelis Pedigrees.Genome biology and evolution · 2025Article
- Characterizing the Rates and Patterns of De Novo Germline Mutations in the Aye-Aye (Daubentonia madagascariensis).Molecular biology and evolution · 2025Article
- Methods for Chromosome-Scale Haplotype Reconstruction.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Resolving complex duplication variants in autism spectrum disorder using long-read genome sequencing.Genome research · 2024Article
- Characterizing the rates and patterns ofbioRxiv : the preprint server for biology · 2024Article
- Automated evaluation of multiple sequence alignment methods to handle third generation sequencing errors.PeerJ · 2024Article
- Article
- Read-Based Phasing and Analysis of Phased Variants with WhatsHap.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Genetic polyploid phasing from low-depth progeny samples.iScience · 2022Article
- Multiallelic models for QTL mapping in diverse polyploid populations.BMC bioinformatics · 2022Article
- Chromosome-Level Haplotype Assembly forFrontiers in genetics · 2022Article
- Computational methods for chromosome-scale haplotype reconstruction.Genome biology · 2021Review
- Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationRead-based phasing deduces the haplotypes of an individual from sequencing reads that cover multiple variants, while genetic phasing takes only genotypes as input and applies the rules of Mendelian inheritance to infer haplotypes within a pedigree of individuals. Combining both into an approach that uses these two independent sources of information-reads and pedigree-has the potential to deliver results better than each individually.
resultsWe provide a theoretical framework combining read-based phasing with genetic haplotyping, and describe a fixed-parameter algorithm and its implementation for finding an optimal solution. We show that leveraging reads of related individuals jointly in this way yields more phased variants and at a higher accuracy than when phased separately, both in simulated and real data. Coverages as low as 2× for each member of a trio yield haplotypes that are as accurate as when analyzed separately at 15× coverage per individual. AVAILABILITY AND IMPLEMENTATION: https://bitbucket.org/whatshap/whatshap CONTACT: t.marschall@mpi-inf.mpg.de.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.