Samtools 1.7 flagstat

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