Does JBrowse support user to load their own custom track from vcf file

[JeanQ2020]

We'd like to find a browser which can allow user to load their own variant file (vcf) stored as temporary session and delete the track when user exits the web. I couldn't find any document that mentions this capacity for JBrowse

[cmdcolin]

@JeanQ2020 Yes, we do allow the user to open their own VCF or other types of files. If the file is large, I recommend using a bgzip+tabix indexed VCF, but for smallish VCF (think megabytes instead of gigabytes), then you can just open a plaintext VCF with the add track button.

I created a video to demonstrate how this works below

This video is using our "demo" browser on jbrowse.org but would apply to an instance if you set it up on your website too

The video shows the following things

a) adding a custom vcf file as a track. this file exists on the users hard drive.
b) then reloading the page. the web browser doesn't allow us to keep that file open after a page reload, but the track still stays alive in the session. so I actually demo manually re-loading it via the Settings menu, then re-performing the Open file for the track. i'm not sure you want that feature or care about it, but it's just how we have it currently.
c) I then navigate to a new session (click the Browse demo button again, this starts a new "session") and the local file track is not there anymore. that is sort of equivalent to the track being deleted when the user exits the web.

video:

out.mp4

[JeanQ2020]

@cmdcolin Thank you so much for your quick response and helpful video. This is definitely what we'd like to see. I have two follow up questions: 1) does unix installation with web version also provide the same functionality for user to load and view their own custom vcf track on their own session (temporarily)? 2) does JBrowse allow long url with params (e.g., chr, coordinates)? We'd like to have ability to link a variant DB tool to JBrowse such that user can click a variant coordinate on that tool to launch and view that variant on JBrowse.

[cmdcolin]

you can try prefixing any command in our docs with "npx" so type "npx @jbrowse/cli create yourfolder". The "npx" command is a "command runner" that will automatically download and run the jbrowse cli tool. I think it works without admin privileges (note that depending on your setup you may run into other challenges without admin permissions like setting up the http server but hopefully this helps)

[garrettjstevens]

I think the command would be npx @jbrowse/cli create yourfolder, since it needs the package name.

[cmdcolin]

thanks updated my comment too!

[JeanQ2020]

@cmdcolin Thanks for your helpful suggestions. Unfortunately it doesn't work for me probably due to permission issue.

[JeanQ2020]

@cmdcolin BTW, we have a virtual wet server that hosts one of our genomics websites using Tripal. It has JBrowse plugin with the genome browse that gets information from its postgresql database. Are you familiar with the jbrowse plugin on Tripal and if you know that it supports loading local custom track? I didn't see the + sign any where on its browse. It'll be great if it can support loading custom tracks.