Question: What is the best method to map snps called using GATK to corresponding genes?
1
gravatar for lakhujanivijay
2.7 years ago by
lakhujanivijay4.4k
India
lakhujanivijay4.4k wrote:

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.

snp gatk gene • 1.3k views
ADD COMMENTlink modified 2.7 years ago by Medhat8.4k • written 2.7 years ago by lakhujanivijay4.4k
0
gravatar for Medhat
2.7 years ago by
Medhat8.4k
Texas
Medhat8.4k wrote:

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


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

ADD COMMENTlink written 2.7 years ago by Medhat8.4k

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?

ADD REPLYlink written 2.7 years ago by lakhujanivijay4.4k

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

ADD REPLYlink written 2.7 years ago by Medhat8.4k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2114 users visited in the last hour