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 Merge BAM-files 

Merge sorted BAM files into a single 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 -> MergeBAMfiles .

Input File(s)

Use  TrmSos_1644_s_1_1.fq.bam and TrmSos_1651_s_2_2.fq.bam from the directory above as test input.

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.


  • Default parameters only, no further configuration needed.

Output File(s)

Expect the an output according to what you set the output name. For the test case, the output file you will find in the example_data directory is named MergedOut.bam. 

Tool Source for App

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