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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mpileup

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Generate pileup for BAM files. Alignment records are grouped by sample identifiers in @RG header lines. If absent, each input file is regarded as one sample. Default settings to skip alignments with mapQ < 10 (remove unmapped/non-unique reads). Output in pileup original format.

Quick Start

Test Data

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Test data for this app appears directly at the link: http://de.iplantcollaborative.org/dl/d/8F3EA44B-AAE5-44B7-8925-42009AF6D852/Out.bam

Input File(s)

Use the file 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)

Expect a Pileup format file as output. For the test case, the output file you will find is as follows: http://de.iplantcollaborative.org/dl/d/72D75676-F3FA-4615-A8CB-6862D3BD8180/Output.pileup

Tool Source for App

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