Question: SNP to gene mapping into reference genome
0
gravatar for sadsam
4.7 years ago by
sadsam0
USA
sadsam0 wrote:

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.

snp • 2.7k views
ADD COMMENTlink modified 4.0 years ago by Biostar ♦♦ 20 • written 4.7 years ago by sadsam0
3
gravatar for Emily_Ensembl
4.7 years ago by
Emily_Ensembl18k
EMBL-EBI
Emily_Ensembl18k wrote:

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

ADD COMMENTlink modified 4.7 years ago • written 4.7 years ago by Emily_Ensembl18k

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.

ADD REPLYlink written 4.7 years ago by sadsam0

Are you using the online tool or the script?

ADD REPLYlink written 4.7 years ago by Emily_Ensembl18k

I am using the online tool. Thanks.

ADD REPLYlink written 4.7 years ago by sadsam0

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.

ADD REPLYlink written 4.7 years ago by Emily_Ensembl18k

Thanks. Looking forward to get the update.

ADD REPLYlink written 4.7 years ago by sadsam0
0
gravatar for Pablo
4.7 years ago by
Pablo1.9k
Canada
Pablo1.9k wrote:

SnpEff also does the trick (http://snpeff.sourceforge.net/)

ADD COMMENTlink written 4.7 years ago by Pablo1.9k

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.

ADD REPLYlink written 4.7 years ago by sadsam0

Which bacteria exactly are you talking about?

ADD REPLYlink written 4.6 years ago by Pablo1.9k
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