title: Analysis of Genotyping-by-Sequencing (GBS) Data.
abstract: The development of genotyping-by-sequencing (GBS) to rapidly detect nucleotide variation at the whole genome level, in many individuals simultaneously, has provided a transformative genetic profiling technique. GBS can be carried out in species with or without reference genome sequences yields huge amounts of potentially informative data. One limitation with the approach is the paucity of tools to transform the raw data into a format that can be easily interrogated at the genetic level. In this chapter we describe bioinformatics tools developed to address this shortfall together with experimental design considerations to fully leverage the power of GBS for genetic analysis.
authors.affiliation: National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, Canada, S7N 0W9.
authors.forename: Sateesh
authors.initials: S
authors.lastname: Kagale
authors.affiliation: National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, Canada, S7N 0W9.
authors.forename: Chushin
authors.initials: C
authors.lastname: Koh
authors.affiliation: Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, Canada, S7N 0X2.
authors.forename: Wayne E
authors.initials: WE
authors.lastname: Clarke
authors.affiliation: Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, Canada, S7N 0X2.
authors.forename: Venkatesh
authors.initials: V
authors.lastname: Bollina
authors.affiliation: Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, Canada, S7N 0X2.
authors.forename: Isobel A P
authors.initials: IA
authors.lastname: Parkin
authors.affiliation: National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, Canada, S7N 0W9. andrew.sharpe@nrc-cnrc.gc.ca.
authors.forename: Andrew G
authors.initials: AG
authors.lastname: Sharpe
mesh_terms: D019295:Computational Biology / Q000379:methods*; D023281:Genomics / Q000379:methods*; D060005:Genotyping Techniques; D012984:Software; D064878:Web Browser
keywords: Bowtie; Demultiplexing, Read map ping; GATK; GBS; Genetic variation; Genotyping; Genotyping -by-sequencing; Haplotype; HaplotypeCaller; Imputation; InDels; Minor allele frequency; Next generation sequencing; RAD-seq; Reduced representation sequencing; SAMtools; Single nucleotide polymorphism; Trimmomatic; UnifiedGenotyper