T3/Oat Genotype Trial description

GBS POGI

  • Description: GBS PstI-MspI, Public Oat Genotyping Initiative, Haplotag
  • Publication: Haplotag: Software for Haplotype-Based GBS Analysis
  • Publication: Haplotype-based GBS in oat genome research
  • Filter: Output was filtered across the full population to maintain markers for which genotype calls were 50% or 80% complete, heterozygosity was 10%, and minor allele frequency was 5%. Additional filters for Haplotag included a maximum base difference of three for aligning tags, a maximum of nine tags per cluster, a maximum heterozygote frequency on a haplotype basis of 0.25, and a maximum tolerance for tri-zygotes and multi-zygotes of 1% and 0%, respectively.

GBS Spain

  • GBS PstI-MspI, Spain, Haplotag
  • Protocol
  • Accessions
  • Genotype file
  • Filter: removed all markers with lower than 80% completeness, less than 5% minor allele frequency, or greater than 10% heterozygosity

GBS Core

Infinium 2010

  • Publication: A SNP Genotyping Array for Hexaploid Oat
  • Filter: filtered SNPs to maximize predicted minor allele frequency (MAF), to minimize heterozygotes within varieties (which could signify miss-assemblies of orthologous and paralogous loci), and to eliminate SNPs that contained multiple variants within the 120- or 200-base context sequence used for assay design

Infinium 2020