prepare a GFF file for MOCK fasta reference

Question

[Sam]

Dear Biostars

I need your help to handle this problem, I'm working with GBS data and now I have a big list of SNP position in my output file and I used a mock reference for SNP variant analysis (merged some of GBS samples to prepare a mock ref). In the output file, I have the position of SNP according to the mock reference, for instance, positions 480, 650, 213546 in the mock reference fasta file. so I need to prepare a GFF file according to genome reference sequence for other subspecies to annotate the SNPs, for example, intronic or exonic SNPs

how can I prepare this file?

Thanks

[h.mon]

You have to look for pre-built chain files (or build them yourself), and then convert the coordinates of the GFF with tools such as liftOver or CrossMap.