What should the BED file format be?

  • Updated

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:

  1. Chromosome number 
  2. Start
  3. Stop
  4. dbSNP ID (any ID)
  5. 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

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