How to build my own snp search database and add a snp track to browser?

[songtaogui]

Hi, @lidaof

I have some local snp.vcf files, and would like to build a snp search function as http://epigenomegateway.wustl.edu/browser/ does. Is there a detail manual for that?

And I have noticed the Snps from ensembl track has a track type of "snp", which was not documented in the doc. How could I display my variantions using washu browser? Should I put the variants into backend monodb ?

Is it possible that the browser can support displaying of vcf format variantions (SVs).

Thank you,

Best wishes,

Songtao Gui

[lidaof]

Hi @songtaogui , the doc mentioned SNP search uses the Ensembl API services: https://rest.ensembl.org if you pull latest code, you can use the track directly. no need to put in backend mongodb.

i am personally not very familiar with vcf format, can you please send me an example file? and how do you want the file to be visualized (an example figure)?

Thank you!

[songtaogui]

So sorry for the late reply, I was quite busy with other stuffs.

The brief introduction of VCF format can be found here

And in Jbrowse, the VCF file was displayed like this:

and Click on each variant item would lead to its detail page like this:

Best wishes

[lidaof]

Hi @songtaogui , thank you for the information, I will think about this. :)