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

Discovery Environment Applications List

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Samtools 1.7 view - Filter mapped or unmapped reads

 Filter a SAM/BAM file for mapped or unmapped reads. 

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_view

Input File(s)

Use sample_1.bam in the directory above as your 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.


  • Select BAM format from the drop down box.
  • Select 'remove unmapped reads' under the 'options' section

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 'filtered_alignments.bam.

Tool Source for App

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