extract SNP flanking region in fasta

[Agostino Leone]

Hi all,

I realized that I need to extract the fasta sequences flanking some of my SNPs (the outliers). I tried bcftools consensus in order to combine the VCF allele information with the reference.fasta used in dDocent (containing only a representative portion of all the samples fasta I have) but it seems doesn't work well for my case.

Does anyone did it already and can help me in the process?

Any help would be extremely appreciated, since I'm stucked in this part!

Best,

Agostino