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SNPeff: Find SNPs that are close to exons?

I'm using SNPeff to annotate my vcf file. The program doesn't provide information about how far away a SNP is from the next coding sequence or am I mistaken?

I'm interested in SNPs that are +-20 up-/downstream of exons.

snp exon
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updated by Biostar Biostar • written by Marvin Marvin

1 answer

You probably can do what you want with BEDTools or BEDOPS - something like betools flank to get regions flanking exons and bedtools intersect to see which SNPs are at those regions.

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written by h.mon h.mon

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