Visualise a variant position in a gene

Question

[Giulio]

Hi there,

I have a set of three rsids coming from the same gene and I would be interested in visualising their position relative to the gene.

The closest software I found to what I want to make is Biodalliance, but I do not think I can visualise more than 1 independent variant at a time without creating a custom track. Is there any other software/approach that would be suitable for this number of variants?

Thank you and sorry if this is trivial!

[vvasta]

this would be a nice feature to add in Genome broswer (as in blat)

Answer 1

[lacb]

There is the NIH variation viewer : https://www.ncbi.nlm.nih.gov/variation/view/

You can upload your .vcf files containing variants and view them along the reference genome and annotation.

Also there's the Python package DnaFeaturesViewer : https://edinburgh-genome-foundry.github.io/DnaFeaturesViewer/

This package requires more work/coding but it can be automated.

Answer 2

[vvasta]

I've got this info on how to do this in Genome browser

You should be able to accomplish this using the Table Browser (http://genome.ucsc.edu/cgi-bin/hgTables) making the following selections:

Select human, and your assembly of interest. The dbSNP155 track exists for both hg19 and hg38. Set the group to "Variation". Set the track to "dbSNP 155". Click identifiers and paste or upload a list containing all your rsIDs. In the output format dropdown select custom track. This should result in a new track on the Genome Browser containing only the rsID variants from our list.