Are there any tools which display SNPs inside each gene?

Question

[bioinforesearchquestions]

Hello friends,

I am planning to map SNPs to a set of genes. I want to represent them in a graphical format.

Are there any tools which display SNPs inside each gene?

[WouterDeCoster]

I'm not sure if I understood your question correctly, but I think MutationMapper might be what you are looking for

[bioinforesearchquestions]

Thanks, WouterDeCoster. I am looking something like this. I have been provided just with 3 columns. 1) rsids

2) genename

3) sequence has been provided if there is no rsids available.

But they need following details,

[WouterDeCoster]

Read again:

Mutation files should be tab delimited, and should at least have the following headers in the first line: -Hugo_Symbol -Protein_Change

Using the rsids you will have to find the required information, which shouldn't be too hard (and there are many threads about converting dbSNP/rsids to something else).

[bioinforesearchquestions]

Hi WouterDecoster, Yeah using rsids, I collected the information from dbSNP. The plot generated by the mutation-mapper doesn't label the mutations with rsids.

My requirement is to label each mutation with rsids and x-axis should be position of the gene.

Answer 1

[Matteo Schiavinato]

I am planning to map SNPs to a set of genes. I want to represent them in a graphical format.

To add up on the comments on your question by Wouter, If you have the SNPs in a VCF file, you already have the coordinates on the reference sequence. If you have a GTF file constructed on that ref sequence, you can load both VCF and GTF to a tool like IGV or GBrowse and browse graphically to the gene regions you want, saving the svg high-quality image.