title: Simple, rapid and accurate genotyping-by-sequencing from aligned whole genomes with ArrayMaker.
abstract: CONCLUSIONS
  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.
  
  
  METHODS
  ArrayMaker is licensed under The MIT License and can be freely obtained at https://github.com/cw2014/ArrayMaker/. The program is implemented in Perl and runs on Linux operating systems.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
  
  
  BACKGROUND
  cali.willet@sydney.edu.au.
authors.affiliation: Faculty of Veterinary Science and School of Information Technologies, University of Sydney, Sydney, New South Wales 2006, Australia.
authors.forename: Cali E
authors.initials: CE
authors.lastname: Willet
authors.affiliation: Faculty of Veterinary Science and School of Information Technologies, University of Sydney, Sydney, New South Wales 2006, Australia.
authors.forename: Bianca
authors.initials: B
authors.lastname: Haase
authors.affiliation: Faculty of Veterinary Science and School of Information Technologies, University of Sydney, Sydney, New South Wales 2006, Australia.
authors.forename: Michael A
authors.initials: MA
authors.lastname: Charleston
authors.affiliation: Faculty of Veterinary Science and School of Information Technologies, University of Sydney, Sydney, New South Wales 2006, Australia.
authors.forename: Claire M
authors.initials: CM
authors.lastname: Wade
mesh_terms: D015894:Genome, Human; D055106:Genome-Wide Association Study; D005838:Genotype; D060005:Genotyping Techniques / Q000379:methods*; D006801:Humans; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software