Extract SNPs from VCF file located in genes or flanking +/- 5Kbp on GFF file

Question

[User000]

Hello,

I have a VCF file with SNPs and genes in GFF file. I would like to extract only SNPs that reside on the genes or flanking +/- 5kb. I could artificially add/substract 5kb to gff file and then follow the answer in this link: https://www.biostars.org/p/333734/), but is there an option to do so? Also, is it possible to append the gene name and positions to the vcf file?

Answer 1

[jared.andrews07]

I'd probably just add the 5kb to the gff via bedtools slop, then intersect with bedtools intersect -wa -wb, and you'd basically have everything you want.

[User000]

yeah... the only minus is that I will have the start and stop +/- 5kb, anyway I decided to add only gene information to the vcf file and not position, thank you :)

[User000]

why in the intersect output vcf file the header is missing?

[jared.andrews07]

Bedtools doesn't preserve headers by default. You can try using the --header option (but it has to be in their specific format), or you can pipe the header to your output file first, then append your results to bedtools to that file. Or just open and tack it on afterwards, which is often easiest if you want to keep the headers from both files after an intersect.