eprintid: 10024540
rev_number: 28
eprint_status: archive
userid: 608
dir: disk0/10/02/45/40
datestamp: 2017-10-08 10:56:10
lastmod: 2021-10-03 23:49:49
status_changed: 2018-01-31 12:45:56
type: article
metadata_visibility: show
creators_name: Tekman, M
creators_name: Medlar, A
creators_name: Mozere, M
creators_name: Kleta, R
creators_name: Stanescu, H
title: HaploForge: a comprehensive pedigree drawing and haplotype visualization web application
ispublished: pub
divisions: UCL
divisions: B02
divisions: C10
divisions: D17
divisions: G93
note: This version is the author accepted manuscript. For information on re-use, please refer to the publisher’s terms and conditions.
abstract: Motivation: Haplotype reconstruction is an important tool for understanding the aetiology of human disease. Haplotyping infers the most likely phase of observed genotypes conditional on constraints imposed by the genotypes of other pedigree members. The results of haplotype reconstruction, when visualized appropriately, show which alleles are identical by descent despite the presence of untyped individuals. When used in concert with linkage analysis, haplotyping can help delineate a locus of interest and provide a succinct explanation for the transmission of the trait locus. Unfortunately, the design choices made by existing haplotype visualization programs do not scale to large numbers of markers. Indeed, following haplotypes from generation to generation requires excessive scrolling back and forth. In addition, the most widely used program for haplotype visualization produces inconsistent recombination artefacts for the X chromosome. / Results: To resolve these issues, we developed HaploForge, a novel web application for haplotype visualization and pedigree drawing. HaploForge takes advantage of HTML5 to be fast, portable and avoid the need for local installation. It can accurately visualize autosomal and X-linked haplotypes from both outbred and consanguineous pedigrees. Haplotypes are coloured based on identity by descent using a novel A* search algorithm and we provide a flexible viewing mode to aid visual inspection. HaploForge can currently process haplotype reconstruction output from Allegro, GeneHunter, Merlin and Simwalk. / Availability and implementation: HaploForge is licensed under GPLv3 and is hosted and maintained via GitHub. https://github.com/mtekman/haploforge / Contact: r.kleta@ucl.ac.uk / Supplementary information: Supplementary data are available at Bioinformatics online.
date: 2017-12-15
date_type: published
publisher: OXFORD UNIV PRESS
official_url: http://dx.doi.org/10.1093/bioinformatics/btx510
oa_status: green
full_text_type: other
language: eng
primo: open
primo_central: open_green
verified: verified_manual
elements_id: 1426503
doi: 10.1093/bioinformatics/btx510
lyricists_name: Kleta, Robert
lyricists_name: Stanescu, Horia
lyricists_id: RKLET98
lyricists_id: HSTAN15
actors_name: Allington-Smith, Dominic
actors_id: DAALL44
actors_role: owner
full_text_status: public
publication: Bioinformatics
volume: 33
number: 24
pagerange: 3871-3877
pages: 7
issn: 1460-2059
citation:        Tekman, M;    Medlar, A;    Mozere, M;    Kleta, R;    Stanescu, H;      (2017)    HaploForge: a comprehensive pedigree drawing and haplotype visualization web application.                   Bioinformatics , 33  (24)   pp. 3871-3877.    10.1093/bioinformatics/btx510 <https://doi.org/10.1093/bioinformatics%2Fbtx510>.       Green open access   
 
document_url: https://discovery.ucl.ac.uk/id/eprint/10024540/1/Kleta_s1-ln27069688.pdf