Sequence of GBS tag

Question

[wdlngtn]

This question may have a very straightforward answer, but I’ve not been able to find it online or in the TASSEL manual.

I would like to design PCR primers around a SNP from GBS data made using the TASSEL pipeline (TASSEL3).

I have the name of the SNP, which indicated the scaffold it’s on, and also the intermediate files from TASSEL. What is the best way to get the physical sequence of one or preferably both alleles of a GBS tag from TASSEL?

Thanks in advance!