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.
2 answers
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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