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 mpileup variant pipeline 

Generate BCF or pileup for one or multiple BAM files. Alignment records are grouped by sample identifiers in @RG header lines. If sample identifiers are absent, each input file is regarded as one sample.

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_mpileup.

Input File(s)

Use ex1.bam and chr8.fa 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.

 

  • Default parameters only, no further configuration needed.

 

Output File(s)

For the test case, the output file you will find in the example_data directory is named samtools_mpileup_out

Tool Source for App

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