Automatic BAM indexing

Question: Automatic BAM indexing

28 days ago by

Dear community,

is there a way to modify the default way Galaxy creates the index *.BAI files? We work with a large salamander genome, therefore, quite some coordinates in the BAM files are beyond 2^30. Therefore, the index files have to be created using either biobambam2:bamSort or samtools index -c -m 14. However, I cannot really figure out if there is a simple way to "teach" Galaxy how to do that. We have our own institute's Galaxy instance, therefore, I can change pretty much anything there...

I am sorry if a similar question was posted before and would be thankful for any advice.

Best regards, Sergej

samtools galaxy bai bam • 68 views

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written 28 days ago by Sergej.Nowoshilow • 0

Hi - I asked the developers for feedback at the Galaxy Project's Gitter channel here: https://gitter.im/galaxyproject/Lobby?at=5bdb2dde5905a9195539cbac

Please feel free to comment/or follow up with more info at Gitter if you want. They might reply here or there or ask for more information. I'll check back and link everything together for the final reply/solution.

Thanks! Jen, Galaxy team

ADD REPLY • link written 27 days ago by Jennifer Hillman Jackson ♦ 25k

27 days ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Even if this was enabled, standard Galaxy tools (from the ToolShed https://usegalaxy.org/toolshed) wouldn't be able to use the data as an input. Are you using custom tools, or do you plan to modify tool wrappers to work with this data as well?

Discussion:

Marius van den Beek @mvdbeek 09:49

Yes, we can generate .csi indexes, but I don't think any galaxy tool would be able to do anything with those at the moment.
I assume the issue is mostly that metadata setting doesn't work for that genome ?

Jennifer Hillman-Jackson @jennaj 09:52

Yes, that is how I understand it. They may have custom tools. I pointed the user to this thread, and will prompt them for more info/intended usage.

Plus more now that follows up on tools, alternate formats: https://gitter.im/galaxyproject/Lobby?at=5bdb2dde5905a9195539cbac

Thanks! Jen, Galaxy team

ADD COMMENT • link modified 26 days ago • written 27 days ago by Jennifer Hillman Jackson ♦ 25k

Yes, I have a set of custom tools and also adjusted some of the tools from the standard ToolShed. However, I have a feeling that many tools may be just fine if the .csi file is renamed to .bai. Those tools rely on HTS library and, therefore, this naming must be completely transparent for them as the library takes care of the rest. However, I never tested it explicitly. It was just an observation, since a few tools including the IGV browser are just fine with this setup.

ADD REPLY • link written 27 days ago by Sergej.Nowoshilow • 0

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