search

igvteam / igv-reports

Python application to generate self-contained pages embedding IGV visualizations, with no dependency on original input files.
MIT License
347 stars 51 forks source link

Sorting option #25

Closed binfyun closed 4 years ago

binfyun commented 5 years ago

Hi,

Is there a way to add more sorting options to the popup window when clicking on the reads.

Thanks

jrobinso commented 5 years ago

Hi @binfyun,

What would you like to sort by?

This is really an igv.js question, but I assume you are using igv.js in the context of igv-reports?

binfyun commented 5 years ago

Hi @jrobinso Firing up IGV Apps and loading BAMs remotely are oftentimes troublesome. Our goal is to be able to quickly and instantly visualize and ascertain certain variants during a meeting with the pathologist.

Sort by insert size and chromosome of mate would be useful 👍

jrobinso commented 5 years ago

@binfyun Yes, that is exactly the use case igv-reports is designed for. Please keep me informed on progress here, it's important for us to know.

I can add those sort options (again, this is really done in igv.js). However you do understand that sorting is for a specific locus (base), alignments that intersect that locus will be sorted by the chosen attribute. Alignments that don't intersect the base are in random order.

binfyun commented 5 years ago

Hi @jrobinso,

Thank you for your responses and I was able to bring up more reads (used the whole bams without downsampling) per track. 👍

There is a minor bug (or not a bug) on the COSMIC link. The COSMIC link always takes you to the expired ID (4006021 I believe?) and does not reflect the actual IDs in the VCF. Was it hardcoded? I was able to manually correct this by replacing each variant's COSMIC IDs in the "igvjs_viewer.html"

Thanks.

jrobinso commented 5 years ago

The link to cosmic is "hardcoded" but the IDs come from the VCF, they are not hardcoded. If you can post a small VCF where the cosmic links are incorrect I will look into it.

On Fri, Apr 19, 2019 at 12:07 PM David YunTe Lin notifications@github.com wrote:

Hi @jrobinso https://github.com/jrobinso,

Thank you for your responses and I was able to bring up more reads (used the whole bams without downsampling) per track.

There is a minor bug (or not a bug) on the COSMIC link. The COSMIC link always takes you to the expired ID (4006021 I believe?) and does not reflect the actual IDs in the VCF. Was it hardcoded? I was able to manually correct this by replacing each variant's COSMIC IDs in the "igvjs_viewer.html"

Thanks.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/igvteam/igv-reports/issues/25#issuecomment-484988728, or mute the thread https://github.com/notifications/unsubscribe-auth/AAHD2HCVE3I2XZA47IYVPODPRIJ7LANCNFSM4HGWHVVQ .

petermchale commented 4 years ago

@jrobinso : has your team implemented "Sort by insert size and chromosome of mate" in igv.js?

jrobinso commented 4 years ago

@petermchale they have, but not released yet, it will be released early next week and I will update this project at that time. Apologies to all for the long delay.

jrobinso commented 4 years ago

@petermchale New sorting options including insert size & chr of mate have been released. The latest igv.js release is https://cdn.jsdelivr.net/npm/igv@2.3.3/dist/igv.min.js. This is now the default for igv-reports.