How to get the gene name/region from a list of positions

Question

[Luther_Blisset]

I have a list of SNP positions:

761155 
4402247
472711
4027247
2867693

I have a gff reference annotation file and a reference fasta file.

How do I simply find the gene name and locus (e.g. "ctpJ", "Rv3743c", respectively; or "Rv3760", "Rv3760" if there is no gene name) where these SNPs occur?

[Ram]

Position data should include both chromosome and position within chromosome. Once you have that, you can use biomaRt to get gene data. Please search the site - that topic has been addressed multiple times.

Answer 1

[jared.andrews07]

Seems like you're looking for the Variant Effect Predictor. The link I've provided is for Mycobacterium_tuberculosis, which is what I presume you want based on the gene name provided. The tool works for any genome in Ensembl though.