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Hai Galaxy Team,
I have created a .sam file using my own tool. I used a custom genome that I
added to the bowtie_indices.loc.
I want to create another tool which will contain 3 steps,
1. samtool view (sam to bam conversion)
2. samtool sort (sorting bam file)
3. samtool index (creating .bai file)
My problem is how the galaxy can know about the index(.bai) file I am creating?
>From one of the mailing list I learn that a bai file is automatically created
>when adding a bam file to the history.
So can I skip the 3rd step(samtool index)?
ie,Whether a .bai file will create automatically when the tool create the
sorted bam file?
If yes,where will be the .bai file?
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