Design primers that discriminate two alleles of a SNP by restriction digestion.
CAPS uses a natural site created/destroyed by the SNP; dCAPS introduces 1-3 mismatches
in the primer to create the site (Neff et al. 2002).
The chromosome list comes from the chosen BLAST database, so the names are always the ones it actually uses. The region is fetched with blastdbcmd; SNP pos must lie inside it, and the database's base there must be one of the two alleles.
REF/ALT are read from the VCF with bcftools and the flank is fetched from the dataset's reference BLAST DB. Enter the chromosome as the VCF spells it — Chr1A for the Chinese Spring datasets, chr1A for Kronos; it is translated to the DB's naming automatically.
WheatOmics 2.0
