Question: prepare a GFF file for MOCK fasta reference
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gravatar for Sam
2.6 years ago by
Sam140
Sam140 wrote:

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

sequence gff genome • 497 views
ADD COMMENTlink written 2.6 years ago by Sam140

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.

ADD REPLYlink written 2.6 years ago by h.mon32k
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