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 SAM to BAM format conversion


Create a BAM file from a SAM alignment file

Quick Start

Test Data

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Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> Samtools-SAMtoSortedBAM.

Input File(s)

Use  BowtieOutput.sam from the directory listed above. 

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

Tool Source for App

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