I have a .bed and .gff file for a bacterial genome of Gardnerella vaginalis. I also have a csv that contains lists of positions where there are mutations. Ex: 10401, 224444.
I want to feed in the position and figure out the gene or intergenic region the mutation is in. So put in 10401 which is the nucleotide position in the genome, and output what gene annotation or region it is.
How do I do this, are there available tools?