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--get stats 

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Perform an idxstats and flagstat analysis of a BAM file

Quick Start

  • To use (SAMTOOLS-0.1.19) index BAM--get stats, import your data in BAM format.

Resources: https://github.com/samtools/samtools


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 bam index file, an idxstat file and a flagstat file as outputs. For the test case, the output files you will find in the example_data directory are sorted.bam.bai, sorted.bam.idxstats, and sorted.bam.flagstat

Tool Source for App

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