The applications listed here are available for use in the Discovery Environment and are documented in: Discovery Environment Manual.

Discovery Environment Applications List

The box below searches only this space.
To search the entire iPlant wiki, enter your query in the box at the upper right.






Skip to end of metadata
Go to start of metadata


(SAMTOOLS-0.1.19) Index BAM file 

Community rating: ?????

Samtools application to index a BAM file.

Quick Start

Test Data


Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> Index_BAM.

Input File(s)

Use sorted.bam from the directory above as test input.

Parameters Used in App

No parameters to set.

Output File(s)

Expect a file named after the bam file (e.g. *.bam, *.bam.bai) For the test case, the output file you will find in the example_data directory is named sorted.bam.bai

Tool Source for App

  • No labels