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Simple, rapid and accurate genotyping-by-sequencing from aligned whole genomes with ArrayMaker

Citation

Willet, CE and Haase, B and Charleston, MA and Wade, CM, Simple, rapid and accurate genotyping-by-sequencing from aligned whole genomes with ArrayMaker, Bioinformatics, 31, (4) pp. 599-601. ISSN 1367-4803 (2015) [Refereed Article]

Copyright Statement

Copyright 2014 The Authors

DOI: doi:10.1093/bioinformatics/btu691

Abstract

Whole-genome sequencing has revolutionized the study of genetics. Genotyping-by-sequencing is now a viable method of genotyping, yet the bioinformatics involved can be daunting if not prohibitive for some laboratories. Here we present ArrayMaker, a user-friendly tool that extracts accurate single nucleotide polymorphism genotypes at pre-defined loci from whole-genome alignments and presents them in a standard genotyping format compatible with association analysis software and datasets genotyped on commercial array platforms. Using this tool, geneticists with only basic computing ability can genotype samples at any desired list of markers, facilitating genome-wide association analysis, fine mapping, candidate variant assessment, data sharing and compatibility of data sourced from multiple technologies.

Item Details

Item Type:Refereed Article
Keywords:ArrayMaker, genotyping, single nucleotide polymorphism
Research Division:Biological Sciences
Research Group:Genetics
Research Field:Genomics
Objective Division:Expanding Knowledge
Objective Group:Expanding Knowledge
Objective Field:Expanding Knowledge in the Biological Sciences
Author:Charleston, MA (Associate Professor Michael Charleston)
ID Code:106991
Year Published:2015
Deposited By:Mathematics and Physics
Deposited On:2016-02-29
Last Modified:2017-11-01
Downloads:0

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