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 1.7 flagstat

Get statistics about a BAM, SAM or CRAM 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 -> Samtools_mapping_stats.

Input File(s)

Use sample_1.bam in the directory above as you input file. 

Parameters Used in App

When the app is run in the Discovery Environment, use the following parameters with the above input file(s) to get the output provided in the next section below.


  • Enter 'alignment_stats.txt' in the 'output file name' field.

Output File(s)

Expect an output with the name you selected in the app. For the test case, the output file you will get is alignment_stats.txt.

Tool Source for App

  • No labels