The dbSNP or custom .bed file with polymorphic regions is used to add a penalty score to primer pairs. It is optional, and the reference can be uploaded even when this file is not available. It should be a BED file with the following 5 columns:
- Chromosome number
- Start
- Stop
- dbSNP ID (any ID)
- Type of SNP (exact, between, range, etc.)
For example:
chr1 225574904 225574923 rs564787626 range
chr1 17358 17361 rs749387668 range
chr1 10177 10177 rs367896724 between
chr1 10352 10352 rs555500075 between
chr1 11007 11008 rs575272151 exact
chr1 11011 11012 rs544419019 exact