SNP to gene mapping into reference genome

Question

[sadsam]

I have a vcf file containing a list of SNPs from a bacterial isolate which was created by comparing it with a reference strain using GATK. Now I want to map these SNPs to the reference strain's genome in order to find their exact location within and around each gene. I cannot find the right tool to do this. I can see the locations of SNPs with respect to gene in IGV but I cannot retrieve the mapping data from IGV. Please suggest me the right and easy tool for getting this SNP to gene mapping.

Answer 1

[Emily]

VEP! Put in your variant genomic positions, find out their gene positions.

[sadsam]

Thanks a lot . I could get my vcf file working with VEP! I get a table with snp positions relative to genes/ transcripts. Could you let me know how I can import all of the transcript ID descriptions along with this table.

[Emily]

Are you using the online tool or the script?

[sadsam]

I am using the online tool. Thanks.

[Emily]

There isn't a way to get this through the online tool (which doesn't surprise me) but there also isn't currently a way to get the descriptions via the script (which does surprise me). I'll have a word with our developers to see if we can get gene descriptions added, although this may be limited to the script.

[sadsam]

Thanks. Looking forward to get the update.

Answer 2

[Pablo]

SnpEff also does the trick

[sadsam]

Thanks, but the database file for our bacteria is missing and we were unable to create one by ourselves. snpEff support was also non-reponsive.

[Pablo]

Which bacteria exactly are you talking about?