Remove Duplicates in BAM Files Element

Remove PCR duplicates from BAM files using SAMTools rmdup.

Element type: rmdup-bam

Parameters

ParameterDescriptionDefault ValueParameter in Workflow FileType
Output directorySelect an output directory. Custom - specify the output directory in the ‘Custom directory’ parameter. Workflow - internal workflow directory. Input file - the directory of the input file.Input file
out-modenumeric
Output BAM nameA name for the output file. If the default or empty value is provided, the output name is the name of the first file with an additional extension.out-namestring
Remove for single-end readsRemove duplicates for single-end reads. By default, the command works for paired-end reads only (-s).Falseremove-single-endboolean
Treat as single-endTreat paired-end reads as single-end reads (-S).Falsetreat_readsboolean

Input/Output Ports

The element has 1 input port:

Name in GUI: Input File
Name in Workflow File: in-file

Slot In GUISlot in Workflow FileType
Source URLurlstring

And 1 output port:

Name in GUI: Output File
Name in Workflow File: out-file

Slot In GUISlot in Workflow FileType
Source URLurlstring
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