What is the best method to map snps called using GATK to corresponding genes?

Question

[lakhujanivijay]

Hi,

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.

Answer 1

[Medhat]

To convert from vcf to bed you can use vcf2bed from here

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To annotate I use SnpEff as long as you have the genome and gtf/gff it will work; but first the tool have command to search if there database contains annotation for your genome of interest

java -jar snpEff.jar databases | less 
or 
java -jar snpEff.jar databases | grep -i "your genome"

after that use the result to annotate your vcf

java -Xmx5g -jar snpEff.jar result_from_previous_step your.vcf > your.ann.vcf

other wise you can use another tools supported by the software to create your annotation database

[lakhujanivijay]

Thanks, I downloaded and checked the database for the presence of my genome of interest (i am looking for sesame indicum) without luck! From a first look at the file, it seems it only supports bacterial genomes. Any further suggestions?

[Medhat]

as I wrote if the database does not exist you can create it easily read Building database section 9