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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.
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.
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