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--get stats 

 Community rating: ?????

Perform an idxstats and flagstat analysis of a BAM file

Quick Start

  • To use (SAMTOOLS-0.1.19) index BAM--get stats, import your data in BAM format.


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 bam index file, an idxstat file and a flagstat file as outputs. For the test case, the output files you will find in the example_data directory are sorted.bam.bai, sorted.bam.idxstats, and sorted.bam.flagstat

Tool Source for App

  • No labels