Haplotype reconstruction from SNP alignment

2003 ◽  
Author(s):  
Lei Li ◽  
Jong Hyun Kim ◽  
Michael S. Waterman
Keyword(s):  
Haplotype Reconstruction

scholarly journals GAMIBHEAR: whole-genome haplotype reconstruction from Genome Architecture Mapping data

2021 ◽  
Author(s):  
Julia Markowski ◽  
Rieke Kempfer ◽  
Alexander Kukalev ◽  
Ibai Irastorza-Azcarate ◽  
Gesa Loof ◽  
...  
Keyword(s):  
Genetic Variants ◽  
Embryonic Stem Cell Line ◽  
Embryonic Stem ◽  
Mouse Embryonic Stem Cell ◽  
Supplementary Information ◽  
Model Organisms ◽  
Genome Architecture ◽  
Chromatin Conformation ◽  
Haplotype Reconstruction ◽  
Allele Specific

Abstract Motivation Genome Architecture Mapping (GAM) was recently introduced as a digestion- and ligation-free method to detect chromatin conformation. Orthogonal to existing approaches based on chromatin conformation capture (3C), GAM’s ability to capture both inter- and intra-chromosomal contacts from low amounts of input data makes it particularly well suited for allele-specific analyses in a clinical setting. Allele-specific analyses are powerful tools to investigate the effects of genetic variants on many cellular phenotypes including chromatin conformation, but require the haplotypes of the individuals under study to be known a-priori. So far however, no algorithm exists for haplotype reconstruction and phasing of genetic variants from GAM data, hindering the allele-specific analysis of chromatin contact points in non-model organisms or individuals with unknown haplotypes. Results We present GAMIBHEAR, a tool for accurate haplotype reconstruction from GAM data. GAMIBHEAR aggregates allelic co-observation frequencies from GAM data and employs a GAM-specific probabilistic model of haplotype capture to optimise phasing accuracy. Using a hybrid mouse embryonic stem cell line with known haplotype structure as a benchmark dataset, we assess correctness and completeness of the reconstructed haplotypes, and demonstrate the power of GAMIBHEAR to infer accurate genome-wide haplotypes from GAM data. Availability GAMIBHEAR is available as an R package under the open source GPL-2 license at https://bitbucket.org/schwarzlab/gamibhear Maintainer [email protected] Supplementary information Supplementary information is available at Bioinformatics online.

scholarly journals Haplotype reconstruction from genotype data using Imperfect Phylogeny

2004 ◽  
Vol 20 (12) ◽  
pp. 1842-1849 ◽  
Author(s):  
E. Halperin ◽  
E. Eskin
Keyword(s):  
Genotype Data ◽  
Haplotype Reconstruction

scholarly journals Saving DNA from museum specimens: The success of DNA mini-barcodes in haplotype reconstruction in the genus Anastrepha (Diptera: Tephritidae)

2019 ◽  
Vol 16 ◽  
pp. 123-134
Author(s):  
Sandra M. Velasco-Cuervo ◽  
Elkin Aguirre-Ramirez ◽  
Jenny Johana Gallo-Franco ◽  
Ranulfo González Obando ◽  
Nancy Carrejo ◽  
...  
Keyword(s):  
Museum Specimens ◽  
Haplotype Reconstruction

scholarly journals A New Statistical Method for Haplotype Reconstruction from Population Data

2001 ◽  
Vol 68 (4) ◽  
pp. 978-989 ◽  
Author(s):  
Matthew Stephens ◽  
Nicholas J. Smith ◽  
Peter Donnelly
Keyword(s):  
Statistical Method ◽  
Population Data ◽  
Haplotype Reconstruction

scholarly journals Accuracy of Haplotype Reconstruction from Haplotype-Tagging Single-Nucleotide Polymorphisms

2005 ◽  
Vol 76 (3) ◽  
pp. 438-448 ◽  
Author(s):  
Julian Forton ◽  
Dominic Kwiatkowski ◽  
Kirk Rockett ◽  
Gaia Luoni ◽  
Martin Kimber ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Nucleotide Polymorphisms ◽  
Haplotype Reconstruction ◽  
Single Nucleotide
Sign in / Sign up

Export Citation Format

Share Document