I have a list of snp's in a vcf file called using
GATK for a plant genome. Now, the objective is to map those SNP's to corresponding genes in the genome (I have the reference genome and corresponding GFF file with me) since I have the SNP positions in the
POS column of vcf along with the chromosome name and not gene name.
What is the best approach to achieve the task? What I could think of is:
vcf to bed conversion (by some tool,
vcftools ?, please suggest if you can) and then getting the corresponding gene names from the GFF file (
bedtools; may be?).
Any other alternative approach?
PS: I googled and found many tools specifically designed to annotate human SNP data, while could not find any for plant.