WhatsHap: fast and accurate read-based phasing

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.

• Publication year

  2016

• Venue

  bioRxiv

• Publication date

  2016-11-02

• Fields of study

  Biology, Computer Science

• Identifiers
  DOI 10.1101/085050
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar

• No claims are published for this paper.

• No concepts are published for this paper.

• Direct determination of diploid genome sequences

  2016cited by this paper
• Haplotype estimation for biobank scale datasets

  2016cited by this paper
• Phased diploid genome assembly with single-molecule real-time sequencing

  2016cited by this paper
• Read-based phasing of related individuals

  2016influential reference
• Rare variant phasing and haplotypic expression from RNA sequencing with phASER

  2016cited by this paper
• Selecting Reads for Haplotype Assembly

  2016cited by this paper
• Reference-based phasing using the Haplotype Reference Consortium panel

  2016cited by this paper
• HapCol: accurate and memory-efficient haplotype assembly from long reads

  2016cited by this paper
• WhatsHap: Weighted Haplotype Assembly for Future-Generation Sequencing Reads

  2015influential reference
• Haplotype-resolved genome sequencing: experimental methods and applications

  2015cited by this paper
• Efficient "pythonic" access to FASTA files using pyfaidx

  2015cited by this paper
• MinION Analysis and Reference Consortium: Phase 1 data release and analysis

  2015cited by this paper
• Probabilistic single-individual haplotyping

  2014cited by this paper
• FastHap: fast and accurate single individual haplotype reconstruction using fuzzy conflict graphs

  2014cited by this paper
• Deep Neural Networks Rival the Representation of Primate IT Cortex for Core Visual Object Recognition

  2014cited by this paper
• WhatsHap: Haplotype Assembly for Future-Generation Sequencing Reads

  2014cited by this paper
• Single haplotype assembly of the human genome from a hydatidiform mole

  2014cited by this paper
• Whole-genome haplotyping approaches and genomic medicine

  2014cited by this paper
• HapTree: A Novel Bayesian Framework for Single Individual Polyplotyping Using NGS Data

  2014cited by this paper
• Resolving the complexity of the human genome using single-molecule sequencing

  2014cited by this paper
• Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel

  2014cited by this paper
• Whole-genome haplotyping using long reads and statistical methods

  2014cited by this paper
• The advantages of SMRT sequencing

  2013cited by this paper
• Saturated linkage map construction in Rubus idaeus using genotyping by sequencing and genome-independent imputation

  2013cited by this paper
• PBSIM: PacBio reads simulator - toward accurate genome assembly

  2013cited by this paper
• Exact algorithms for haplotype assembly from whole-genome sequence data

  2013cited by this paper
• A highly accurate heuristic algorithm for the haplotype assembly problem

  2013cited by this paper
• Haplotype assembly in polyploid genomes and identical by descent shared tracts

  2013cited by this paper
• Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM

  2013cited by this paper
• Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls

  2013influential reference
• Haplotype-based variant detection from short-read sequencing

  2012cited by this paper
• An Efficient Algorithm for Haplotype Inference on Pedigrees with Recombinations and Mutations

  2012cited by this paper
• A linear complexity phasing method for thousands of genomes

  2011cited by this paper
• Cython: The Best of Both Worlds

  2011influential reference
• The importance of phase information for human genomics

  2011cited by this paper
• A framework for variation discovery and genotyping using next-generation DNA sequencing data

  2011influential reference
• Haplotype phasing: existing methods and new developments

  2011cited by this paper
• Theory and Algorithms for the Haplotype Assembly Problem

  2010cited by this paper
• Solving VLSI design and DNA sequencing problems using bipartization of graphs

  2010cited by this paper
• Optimal algorithms for haplotype assembly from whole-genome sequence data

  2010cited by this paper
• Global patterns of cis variation in human cells revealed by high-density allelic expression analysis

  2009cited by this paper
• HapCUT: an efficient and accurate algorithm for the haplotype assembly problem

  2008cited by this paper
• The Diploid Genome Sequence of an Individual Human

  2007cited by this paper
• Modeling linkage disequilibrium and identifying recombination hotspots using single-nucleotide polymorphism data.

  2003cited by this paper
• Algorithmic strategies for the single nucleotide polymorphism haplotype assembly problem

  2002cited by this paper
• Merlin—rapid analysis of dense genetic maps using sparse gene flow trees

  2002cited by this paper

• Substantial genomic and methylation variability between MCF-7 sublines

  2026influential citation
• Analytical and clinical validation of CancerMaster, an automated targeted NGS panel, for tumor-only precision oncology

  2026cites this paper
• Rapid Identification of Drug-Resistant Tuberculosis Using Nanopore Targeted Next-Generation Sequencing from Sputum and Culture Isolates: Accuracy and Limitations

  2026cites this paper
• B cell phenotypes and antibody signatures associate with interpatient variation in the lung adenocarcinoma tumor microenvironment

  2026cites this paper
• LORA: a Polymorphic Multi-sample Long Read Assembly Pipeline

  2026cites this paper
• Comparative evaluation of an original microhaplotype panel and its expanded version for human identification and ancestry inference in Brazilian and admixed American populations.

  2026cites this paper
• In vivo lineage tracing across human tissues using methylation barcodes in the protocadherin gene cluster

  2026cites this paper
• Leveraging ONT move table values for signal aware variant calling

  2026cites this paper
• HapBridge: A Methylation-Guided Approach for Correcting Switch Errors and Bridging Phased Blocks in Long-Read Phasing

  2026cites this paper
• Ongoing chromothripsis underpins osteosarcoma genome complexity and clonal evolution.

  2025cites this paper
• STRkit: precise, read-level genotyping of short tandem repeats using long reads and single-nucleotide variation

  2025cites this paper
• Biallelic variants in RNU2-2 cause the most prevalent known recessive neurodevelopmental disorder

  2025cites this paper
• Nanopore sequencing-based genotyping suggested an association between CYP2D6 function and susceptibility to anxiety and depression

  2025cites this paper
• Long-read sequencing reveals novel genetic polymorphisms in the major histocompatibility complex region and their impacts on the Han Chinese population

  2025influential citation
• Cell type-specific epigenomic variation and its association with genotype in the human breast

  2025cites this paper
• Chromosomal Inversions Mediated by Tandem Insertions of Transposable Elements

  2025cites this paper
• Isoform analysis of heterozygous putative splicing variants at the allele level using nanopore long-read sequencing

  2025cites this paper
• Severus detects somatic structural variation and complex rearrangements in cancer genomes using long-read sequencing

  2025cites this paper
• kir‐mapper: A Toolkit for Killer‐Cell Immunoglobulin‐Like Receptor (KIR) Genotyping From Short‐Read Second‐Generation Sequencing Data

  2025influential citation
• A lectin receptor-like kinase controls self-pollen recognition in Phlox (Polemoniaceae)

  2025cites this paper
• Haplotypic resolution of the challenging genomic regions of MHC and KIR using a combination of targeted sequencing and a novel assembly pipeline

  2025influential citation
• From genotype to phenotype with 1,086 near telomere-to-telomere yeast genomes

  2025cites this paper
• SAVANA: reliable analysis of somatic structural variants and copy number aberrations using long-read sequencing

  2025cites this paper
• Structural variation in 1,019 diverse humans based on long-read sequencing

  2025cites this paper
• Repeated polyploidization shapes divergence in floral morphology in Lithophragma bolanderi (Saxifragaceae)

  2025influential citation
• Incomplete recombination suppression fuels extensive haplotype diversity in a butterfly colour pattern supergene

  2025cites this paper
• SEC24C deficiency causes trafficking and glycosylation abnormalities in an epileptic encephalopathy with cataracts and dyserythropoeisis

  2025cites this paper
• Investigation of a pathogenic inversion in UNC13D and comprehensive analysis of chromosomal inversions across diverse datasets

  2025cites this paper
• Agrobacterium-derived DNA sequences in phylogenetic studies of plants

  2025cites this paper
• Recent rapid radiation of apex predators suggests dramatic biodiversity turnover in an ancient lake

  2025cites this paper
• High-coverage allele-resolved single-cell DNA methylation profiling reveals cell lineage, X-inactivation state, and replication dynamics

  2025cites this paper
• Whole genome sequencing of pre-treatment and post-treatment locally advanced rectal cancer using long and short read technologies

  2025cites this paper
• The Roles of Life History and Mating System in Speciation: Genomic Evidence From the Incarvillea sinensis Complex

  2025cites this paper
• Host range expansion of asexual parasite can be explained by loss of adaptions in Muller’s Ratchet

  2025cites this paper
• The landscape of allele-specific expression in human kidneys

  2025cites this paper
• Complete genomes of a multi-generational pedigree to expand studies of genetic and epigenetic inheritance

  2025influential citation
• ralphi: a deep reinforcement learning framework for haplotype assembly

  2025influential citation
• Leveraging a phased pangenome for haplotype design of hybrid potato

  2025cites this paper
• Merging High-Throughput, Amplicon-Based Second and Third Generation Sequencing Data: An Integrative and Modular Data Analysis Framework for Haplotype Prediction and Output Evaluation

  2025influential citation
• Genome-wide analysis of FSHD cell lines using Nanopore sequencing reveals allele-specific differences at DUX4 target genes and complex repeats

  2025cites this paper
• Computational analysis of DNA methylation from long-read sequencing

  2025cites this paper
• Genome-wide allele-specific expression in multi-tissue samples from healthy male baboons reveals the transcriptional complexity of mammals

  2025cites this paper
• Germline mutation rates and fine-scale recombination parameters in zebra finch

  2025cites this paper
• Complex structural variant visualization with SVTopo

  2025cites this paper
• Long‐Read Whole‐Genome Sequencing Uncovers a Deletion Upstream to HOXD13 Causing Synpolydactyly

  2025cites this paper
• A haplotype-resolved view of human gene regulation

  2025cites this paper
• Targeted long-read methylation analysis using hybridization capture suitable for clinical specimens

  2025cites this paper
• Diploid donor-specific assembly enhances somatic structural variant detection in cancer genomes

  2025cites this paper
• Long-read transcriptome analysis using IsoRanker for identifying pathogenic variants in Mendelian conditions

  2025cites this paper
• A Case of Salt-Wasting Congenital Adrenal Hyperplasia Caused by a Rare Intronic Variant in the CYP21A2 Gene

  2025influential citation
• Benchmarking imputation accuracy in the presence or absence of a reference panel

  2025cites this paper
• Indel calling from ONT sequencing data of family trios via sparse attention and 3D convolution

  2025cites this paper
• Blended Length Genome Sequencing (blend-seq): Combining Short Reads with Low-Coverage Long Reads to Maximize Variant Discovery

  2025cites this paper
• D4Z4End2End: complete genetic and epigenetic architecture of D4Z4 macrosatellites in FSHD, BAMS and reference cohorts

  2025cites this paper
• Long-read sequencing of single cell-derived melanoma subclones reveals divergent and parallel genomic and epigenomic evolutionary trajectories

  2025cites this paper
• Habitat Specialisation Impacts Clownfish Demographic Resilience to Pleistocene Sea‐Level Fluctuations

  2025cites this paper
• bloodAGENT: a versatile tool for blood group typing and genomic variation analysis

  2025cites this paper
• Evidence for a transgenerational mutational signature from ionizing radiation exposure in humans

  2025influential citation
• Genomic bases of short-term evolution in the wild revealed by long-term monitoring and population-scale sequencing

  2025cites this paper
• Genotype imputation from low-coverage WGS using haplotype reference panels in cultivated strawberry

  2025cites this paper
• Interplay of the Genetic Variants and Allele Specific Methylation in the Context of a Single Human Genome Study

  2025cites this paper
• Single-workflow Nanopore whole genome sequencing with adaptive sampling for accelerated and comprehensive pediatric cancer profiling

  2025cites this paper
• Chromosome-level haplotype-resolved assembly of highly heterozygous grass genomes with PhaseGrass

  2025influential citation
• Singleton rapid long-read genome sequencing as first tier genetic test for critically Ill children with suspected genetic diseases

  2025influential citation
• Locityper enables targeted genotyping of complex polymorphic genes

  2025cites this paper
• A telomere-to-telomere map of somatic mutation burden and functional impact in cancer

  2025cites this paper
• Continental-scale genomic surveillance of Plasmodium falciparum malaria with rapid nanopore sequencing

  2025cites this paper
• Benchmarking long-read RNA-sequencing technologies with LongBench: a cross-platform reference dataset profiling cancer cell lines with bulk and single-cell approaches

  2025cites this paper
• Leveraging long-read sequencing technologies for pharmacogenomic testing: applications, analytical strategies, challenges, and future perspectives

  2025cites this paper
• ImputePGTA: accurate embryo genotyping and polygenic scoring from ultra-low-pass sequencing

  2025cites this paper
• Identification of de novo variants from parent-proband duos via long-read sequencing

  2025cites this paper
• Haplotype-resolved diploid genome inference on pangenome graphs

  2025cites this paper
• Population Genomics of Japanese Macaques (Macaca fuscata): Insights Into Deep Population Divergence and Multiple Merging Histories

  2025influential citation
• CRISPR-Cas9-induced double-strand breaks disrupt maintenance of epigenetic information

  2025influential citation
• Induced and natural variation affect traits independently in hybrid Populus

  2024influential citation
• Case report: Deep sequencing and long-read genome sequencing refine prior genetic analyses in families with apparent gonadal mosaicism in PIK3CD-related activated PI3K delta syndrome

  2024cites this paper
• Population genomic evidence of a putative ‘far-west’ African cryptic taxon in the Anopheles gambiae complex

  2024influential citation
• Haplotype-based pangenomes reveal genetic variations and climate adaptations in moso bamboo populations

  2024cites this paper
• Somatic mutation phasing and haplotype extension using linked-reads in multiple myeloma

  2024cites this paper
• Low-pass nanopore sequencing for measurement of global methylation levels in plants

  2024cites this paper
• CRISPR screening uncovers a long-range enhancer for ONECUT1 in pancreatic differentiation and links a diabetes risk variant

  2024cites this paper
• Evolutionary Fate of the Opine Synthesis Genes in the Arachis L. Genomes

  2024influential citation
• Long-read genome sequencing and variant reanalysis increase diagnostic yield in neurodevelopmental disorders

  2024influential citation
• Integration of CTCF loops, methylome, and transcriptome in differentiating LUHMES as a model for imprinting dynamics of the 15q11-q13 locus in human neurons

  2024cites this paper
• Specialization into Host Sea Anemones Impacted Clownfish Demographic Responses to Pleistocene Sea Level Changes

  2024cites this paper
• Quantification of escape from X chromosome inactivation with single-cell omics data reveals heterogeneity across cell types and tissues

  2024cites this paper
• Approach for Phased Sequence-Based Genotyping of the Critical Pharmacogene Dihydropyrimidine Dehydrogenase (DPYD)

  2024cites this paper
• Exploring the role of polymorphic interspecies structural variants in reproductive isolation and adaptive divergence in Eucalyptus

  2024cites this paper
• Multiple hybridization events and repeated evolution of homoeologue expression bias in parthenogenetic, polyploid New Zealand stick insects

  2024influential citation
• Long-read whole-genome sequencing-based concurrent haplotyping and aneuploidy profiling of single cells

  2024influential citation
• Genomic Analyses Capture the Human-Induced Demographic Collapse and Recovery in a Wide-Ranging Cervid

  2024cites this paper
• A deep intronic variant in MME causes autosomal recessive Charcot–Marie–Tooth neuropathy through aberrant splicing

  2024cites this paper
• HapKled: a haplotype-aware structural variant calling approach for Oxford nanopore sequencing data

  2024cites this paper
• Genomic insights on conservation priorities for North Sea houting and European lake whitefish (Coregonus spp.)

  2024influential citation
• A deep intronic variant in MME causes autosomal recessive Charcot-Marie-Tooth neuropathy through aberrant splicing

  2024cites this paper
• Figeno: multi-region genomic figures with long-read support

  2024cites this paper
• Unravelling undiagnosed rare disease cases by HiFi long-read genome sequencing

  2024influential citation
• A case of an Angelman-syndrome caused by an intragenic duplication of UBE3A uncovered by adaptive nanopore sequencing

  2024cites this paper
• KSNP: a fast de Bruijn graph-based haplotyping tool approaching data-in time cost

  2024cites this paper
• Scalable telomere-to-telomere assembly for diploid and polyploid genomes with double graph

  2024cites this paper