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 1.7 mpileup

Generate BCF or VCF for one or more 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


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 from the directory above as bam input and ex1.fa from the directory above as reference sequence.

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.
  • Enter 'samtools_mpileup_output'  in the 'output file name' field. 

Output File(s)

Expect 'samtools_mpileup_output' as output.

Tool Source for App

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