- The ~51K SNPs on the iSelect Illumina genotyping platform Muñoz-Amatriaín et al. 17 have positional information relative to the cowpea reference genome IT97K-499-35 but not all positions are accurate. There is limited information on gene names, the class of variants, etc. We will use two primary annotation tools to identify SNP positions and gene names.
- SNP_Utils implements multiple approaches for the identification of SNP positions. This is a fork of Paul Hoffman's original SNP_Utils
- The repository for updating the barley Morex reference also contains useful code morex_reference.
- SNPMeta is a BLAST parser that identifies the genes in which SNPs occur and can identify the nature of mutations (e.g., synonymous versus nonsynonymous). SNPMeta design and usage is detailed in Kono et al. 2014.
- VeP annotations have been applied for all SNP positions indentified for the original iSelect design file