Re: [Gmod-ajax] JBrowse 2 guide

[Ke J. <bio...@gm...>]

Sounds great! Thanks!

On Mon, Nov 9, 2020 at 12:02 PM Colin <col...@gm...> wrote:

> 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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>