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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Convert SAM-to-sorted-BAM

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

Quick Start

Test Data

Input File(s)

Use the file 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 a BAM file as output. For the test case, the output file you will find at the link: http://de.iplantcollaborative.org/dl/d/83AA386F-46D9-4769-881A-1F93761EBCF3/output.bam

Tool Source for App

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