[Bug report] drs:// path TCGA bams incompatible with IGV web solutions
Hi Terra,
TCGA bams hosted through drs:// paths work with neither web solutions for IGV suggested by this article nor using local IGV. This was tested with data from several of the controlled access workspaces. TCGA bams not hosted on drs:// paths seem to be working fine. Using whole-exome sequencing from this workspace,
- The bams are not shown as an option to load when using the data model (see the screenshot titled option 1)
- When attempting to follow the procedure for the IGV web app, the web application does not recognize the drs:// paths (see screenshot titled option 2). I also resolved the drs path to get the underlying gsutil path and, upon trying that, the web application returns an access denied error (see screenshot titled option 3).
- When using local IGV, neither the drs:// path not resolved path work (screenshots titled option 4 and 5).
Our group has dealt with this by authorizing our broad emails with ISB-CGC; however, we have been told that ISB-CGC is phasing out support for controlled access TCGA data.
(option 1)
(option 2)
(option 3)
(option 4)
(option 5)
Comments
2 comments
Hi Brendan Reardon,
Thanks for reaching out. It seems like the issue here is that Terra IGV isn't recognizing the BAM/BAI files because the drs:// paths do not include the .bam/.bai file extensions. I've filed a feature request for the Terra IGV app to be able to recognize the DRS links. I'll be sure to let you know of any updates.
As for the IGV web app, the access error you are seeing when using the resolved gs:// paths is expected. DRS links have two components - location of data and authorization - so using the gs:// path alone wouldn't work. Unfortunately, we on the Terra-side don't support the web browser version of IGV (or local version), so I am unable to speak to whether this can be resolved. I would suggest posting your question on the IGV forum here: https://groups.google.com/g/igv-help.
Best,
Samantha
Thank you, Samantha. I created a post on the IGV forums, per your suggestion.
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