How can I get the flanking sequence of SNPs generated from GBS?

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Albino Bacolla

If you have the genomic sequencing data you can use the UCSC tools to transform your fasta files into a single 2bit file and then use twoBitToFa to get your sequences.

Gregor Steve

Thank you so much for your helpful answer. I will try it.

Frederic Lepretre

Hi, if you have the positions you can also try to get the flanking sequences with the UCSC table browser (your positions +/- what you need...output format as sequence...).

fred

Thanks Frederic and Milos for your kind suggestion. I will try

Sorry colleagues, I am working on wheat and not Barley