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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.
http://dev.list.galaxyproject.org/question-about-bam-and-bai-td4136797.html

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?

Regards,
Deepthi.


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