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

journal contribution
posted on 2023-05-18, 17:27 authored by Willet, CE, Haase, B, Michael CharlestonMichael Charleston, Wade, CM
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.

History

Publication title

Bioinformatics

Volume

31

Issue

4

Pagination

599-601

ISSN

1367-4803

Department/School

School of Natural Sciences

Publisher

Oxford Univ Press

Place of publication

Great Clarendon St, Oxford, England, Ox2 6Dp

Rights statement

Copyright 2014 The Authors

Repository Status

  • Restricted

Socio-economic Objectives

Expanding knowledge in the biological sciences

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