get flanking sequences of a SNP in a vcf

Question

[erl1977]

Hi All,

I think something like this has been asked before, but I having trouble finding a simple solution. Essentially, I'm trying to take a VCF, and for each variant in it, I would like to get the flanking ~25nts of the site on either side of the SNP. I would like there to be 2 sequences, 1 with the reference allele in the middle and a second sequence with the the alternate allele in the middle. I would think that there was some application to do this, without me having to re-invente the wheel!

Thanks for any help

[Ram]

It will be a pain but you could iterate variant by variant, use each variant as a VCF format entry somehow with bcftools consensus that picks the appropriate region based on POS of that variant. May I ask why you wish to do this?

Answer 1

[Pierre Lindenbaum]

I wrote https://jvarkit.readthedocs.io/en/latest/Biostar251649/ for Annotating the two flanking bases of SNPs in a VCF file (perhaps SnpEff?) .