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  • Remove Duplicates in BAM Files Element
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Remove PCR duplicates of BAM files using SAMTools rmdup.

Parameters in GUI

ParameterDescriptionDefault value
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
Output BAM nameA name of an output file. If default of empty value is provided the output name is the name of the first file with additional extention. 
Remove for single-end readsRemove duplicate for single-end reads. By default, the command works for paired-end reads only (-s).False
Treat as single-end

Treat paired-end reads and single-end reads (-S).


Parameters in Workflow File 

Type: rmdup-bam

ParameterParameter in the GUIType
out-modeOutput directorynumeric
out-nameOutput file namestring
remove-single-endRemove for single-end readsboolean
treat_readsTreat as single-endboolean

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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