Re: [Gmod-ajax] JBrowse 2 guide

[Colin <col...@gm...>]

Really glad to hear the interest in JBrowse 2!
This is actually a great question and could deserve a tutorial on our
website just for this

Our current docs on this include
- User guide https://jbrowse.org/jb2/docs/user_guide
- SV inspector section of the user guide
https://jbrowse.org/jb2/docs/user_guide#sv-inspector

The SV inspector is currently designed for TRA and BND type events in the
VCF, so any SV caller that outputs TRA (sniffles for example) or breakends
aka BND (pbsv, manta, etc). The SV inspector currently accepts a plain text
VCF instead of gzipped just FYI

Note that you mention the direct visualization of inversion/deletion, which
is shown in our demos. This feature specifically linking of the
supplementary alignments is still on a branch
https://github.com/GMOD/jbrowse-components/pull/1231

Once that branch is merged it will be much better at the "direct
visualization of deletions/inversions" etc.

Let me know if that helps

-Colin

On Mon, Nov 9, 2020 at 10:17 AM Ke Jiang <bio...@gm...> wrote:

> Hi,
>
> I just gave my first try of JBrowse 2, and it works great for most of the
> basic tracks and data types! I'm very interested in the structural variant
> features shown in the demo, such as direct visualization of deletions,
> inversions and translocations. Is there a more detailed guide or
> documentation for these? Do we need a specific variant caller or specific
> format of VCF to work with the BAMs, etc?
>
> Thanks for a great step forward for JBrowse!
>
> Ke
>
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