galaxyproject/tools-devteam

Where is Samtools index?

Closed this issue · 8 comments

alexlenail commented

I installed the samtools 1.2 suite on my galaxy, but one of the functions I use in my local script, samtools index, isn't in the suite. Samtools docs here. Am I just missing it, or is it not included in the suite?

peterjc commented

Galaxy likes to keep all BAM files as sorted BAM, so there is no need to explicitly call samtools index.

alexlenail commented

To visualize the bam file later in tools like IGV the software typically requests a .bai file. Is there a workaround in Galaxy?

peterjc commented

Does this work for you?

  1. Open Galaxy
  2. Click on BAM file in history
  3. Click on disk icon (Download)
  4. Mini menu appears with download links for the BAM and the BAI file
  • 👍1
alexlenail commented

Thanks!

peterjc commented

Yay. Solved.

bgruening commented

@zfrenchee also please note that Galaxy can directly stream you BAM file to your IGV instance. There is no need to download BAM file to visualize them.

peterjc commented

So just copy and paste the URL for the BAM file into IGV (or many other BAM viewers able to take a remote file)?

bgruening commented

@peterjc You can enable this in Galaxy natively. There will be a link on you BAM datasets called: display in IGV local