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

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) Index BAM--get stats

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 Community rating: ?????

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 ___ formatBAM format.

Resources:

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 https://

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github.com/samtools/samtools


Test Data

Info

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

Input File(s)

Use TerriblyIncomprehensible.txt and HorriblyWritten.txt from sorted.bam from the directory 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.

Use either the "Default parameters..." section OR fill in the "Use these parameters..." section. Delete the unused section and the OR. Then, delete this note.

OR

No parameters to set.

Output File(s)

Expect a text file named after the input files as outputbam index file, an idxstat file and a flagstat file as outputs. For the test case, the output file files you will find in the example_data directory is named BeautifulProse.txt.are sorted.bam.bai, sorted.bam.idxstats, and sorted.bam.flagstat

Tool Source for App