get flanking sequences of a SNP in a vcf
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
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Pierre Lindenbaum
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erl1977 •
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erl1977 •
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I wrote https://jvarkit.readthedocs.io/en/latest/Biostar251649/ for Annotating the two flanking bases of SNPs in a VCF file (perhaps SnpEff?) .
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It will be a pain but you could iterate variant by variant, use each variant as a VCF format entry somehow with
bcftools consensusthat picks the appropriate region based on POS of that variant. May I ask why you wish to do this?