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 Sort Bam file

Sort Bam is a function of samtools. Sort alignments by leftmost coordinates or by read names. 

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_sort_BAM.

Input File(s)

Use sample_1.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.

Set the output file name by editing the text "output_prefix" or leave it unedited, for an output file named output_prefix.bam.

Output File(s)

Expect a bam as output. For the test case, the output file you will find in the example_data directory is named output_sorted.bam

Tool Source for App