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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SAM to sorted BAMv2

Create a position-sorted BAM file from a SAM alignment file

App Creator

Roger Barthelson

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 section below.

  • Default parameters only, no further configuration needed.

Output File(s)

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

Related Tutorials

Discover Variants Using SAM Tools (Workflow Tutorial)

Tool Source for App

http://www.htslib.org/

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