HapCUT protocols

View HapCUT computational protocol

HapCUT statistics

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HapCUT specifications


Unique identifier OMICS_00198
Name HapCUT
Alternative name HASH (Haplotype Assembly for Single Human)
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data Some reads aligned to a reference genome.
Input format BAM, VCF
Operating system Unix/Linux
Programming languages C, C++, Perl, Python
Computer skills Advanced
Version 1.0
Stability Stable
Maintained Yes



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  • person_outline Vikas Bansal <>
  • person_outline Vikas Bansal <>

Additional information


Publications for HapCUT

HapCUT in pipeline

PMCID: 4937318
PMID: 27095193
DOI: 10.1093/nar/gkw284

[…] original clones. we only analyzed the results for chromosome 1 of the human genome because of a limited computation capability., to assemble haplotype contigs based on the allele-assigned results, hapcut () required both clone sequences and the corresponding variant set. the clones were selected first, each of which carried more than one allele and was located in chromosome 1., in the clone […]

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HapCUT in publications

PMCID: 5954289
PMID: 29764364
DOI: 10.1186/s12864-018-4464-9

[…] and the predicted haplotypes is minimized (such objective function is called minimum error correction, or mec). many methods have been proposed for the diploid haplotype phasing problem: hash [] and hapcut [] are based on graph structure. he et al. [] proposed a dynamic programming method as well as a max-sat formulation. deng et al. [] combined this dynamic programming method with a heuristic […]

PMCID: 5903673
PMID: 29621242
DOI: 10.1371/journal.pgen.1007308

[…] mapping., shapeit with parental genotype data. in addition to the individual’s genotype to be phased, the parental genotype data were supplied and phased together using a haplotype reference panel., hapcut (version 0.7 updated on 9/11/2013) with the wgs reads. this computational phasing algorithm addresses haplotype phasing as a haplotype assembly problem using dna sequence fragments rather […]

PMCID: 5703283
PMID: 29078313
DOI: 10.1073/pnas.1707609114

[…] illumina wgs data of pgp1 fibroblast cells (under encode project “encsr674pqi”), was used to phase the 1.2 million snps in sissor fragments. we applied these snps to a haplotyping algorithm, hapcut2 (), and compared the assembly to the pgp1 haplotype created using subhaploid pools of bac clones (). two types of errors may occur in an assembled haplotype. first, a switch error was defined […]

PMCID: 5261742
PMID: 28068346
DOI: 10.1371/journal.pgen.1006550

[…] statistical difference between mating systems via fisher’s tests (h0 and d) or z-tests of odds-ratios differences (dconstrained/dneutral ratios). both tests were accomplished with r base functions., hapcut v0.7 [] was used to generate haplotypes in all apomictic samples using a max insert size of 600. for each pair of hapcut-split apomictic haplotypes, a three-sequence alignment was built, […]

PMCID: 5179053
PMID: 28005948
DOI: 10.1371/journal.pgen.1006433

[…] data from leaves, phloem, flowers and fruits of ‘junzao.’ the snp calling results derived from the resequencing of 31 accessions were used to reconstruct the two haplotypes of s-rnase gene using hapcut []., phloem, mature leaves, flowers, and fruits at different stages (expanding fruit, half-red, and full-red) of the ‘junzao’ cultivar and the wild jujube ‘qingjiansuanzao’ (8 years old) […]

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HapCUT institution(s)
Department of Computer Science and Engineering, University of California, San Diego, CA, USA

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