I’m in Cavatica and I would like to use the Genome Browser to visualize some regions of the BAM files from the neuroblastoma cohort. The Genome Browser requires an index file for each BAM.
Are index files already available for the BAM files generated by Kids First? If so, where can I find them?
I see that I can use the BamTools Index task to create index files, but that would be a lot of redundant effort if each user has to create their own.
I am going to reply to myself here and say that it looks like the intended use of Kids First alignment files is for each user to create their own index. I say this based this paragraph from the Kids First DRC Help Center on the topic of storage costs:
There are no storage costs for Kids First files on Cavatica that are sent from the portal.
All other files in Cavatica projects incur storage costs. These include files that users upload to the project and any output that is generated by user workflows. User-generated files associated with Kids First files (for example, an index file that is generated from a Kids First alignment file) fall under this category and will contribute toward storage costs.
This sounds to me like the alignment files are expected to be used in common (with hard links in the file system, I suppose) but the associated index files will have be generated and stored for each user.
I’ll say, again, that it seems wasteful of compute time and storage. Is there a good reason for this?