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-0.1.19) Index BAM file 

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Samtools application to index a BAM 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 -> Index_BAM.

Input File(s)

Use sorted.bam from the directory above as test input.

Parameters Used in App

No parameters to set.

Output File(s)

Expect a file named after the bam file (e.g. *.bam, *.bam.bai) For the test case, the output file you will find in the example_data directory is named sorted.bam.bai

Tool Source for App

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