SNP to gene mapping into reference genome
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10.3 years ago
sadsam ▴ 50

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 • 5.5k views
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10.3 years ago
Emily 24k

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

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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.

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Are you using the online tool or the script?

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I am using the online tool. Thanks.

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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.

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Thanks. Looking forward to get the update.

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10.3 years ago
Pablo ★ 1.9k

SnpEff also does the trick

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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.

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Which bacteria exactly are you talking about?

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