Remove PCR duplicates of BAM files using SAMTools rmdup.
Parameters in GUI
Parameter | Description | Default value |
---|---|---|
Output directory | Select 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 name | A 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 reads | Remove 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). | False |
Parameters in Workflow File
Type: rmdup-bam
Parameter | Parameter in the GUI | Type |
---|---|---|
out-mode | Output directory | numeric |
out-name | Output file name | string |
remove-single-end | Remove for single-end reads | boolean |
treat_reads | Treat as single-end | boolean |
Input/Output Ports
The element has 1 input port:
Name in GUI: Input File
Name in Workflow File: in-file
Slots:
Slot In GUI | Slot in Workflow File | Type |
---|---|---|
Source URL | url | string |
And 1 output port:
Name in GUI: Output File
Name in Workflow File: out-file
Slots:
Slot In GUI | Slot in Workflow File | Type |
---|---|---|
Source URL | url | string |