API for searching for adjacent genes

Question

[VictoriaP]

Hi, is anyone able to advise whether there is an API available to find adjacent upstream or downstream genes from a given gene location?

I am looking at viral insertions in the human genome, and once I've identified the viral insertion points, I need to identify what genes are in the flanking regions.

Any advice is appreciated. Thank you

Answer 1

[WouterDeCoster]

I would get a bed file of human genes and use bedtools closest

[VictoriaP]

Do you know how to create a BED file from a VCF file? - I have multiple vcf files with viral insertion data, that I need to use to make a BED file to then use with bedtools as you previously suggested.