filter pileup

filter pileup

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Remove lines from pileup file that have a mapping coverage of 0

Quick Start

• To use filter pileup, import your data in pileup format.
• Resources: http://samtools.sourceforge.net/pileup.shtml
• http://samtools.sourceforge.net/mpileup.shtml

Test Data

Input File(s)

Use the linked 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 filtered pileup file as output. For the test case, the output file you will find at the link: http://de.iplantcollaborative.org/dl/d/9C69C131-35A5-4ACA-AA67-476C12B5017C/Filtered.pileup

Tool Source for App

• http://sourceforge.net/projects/samtools/files/