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 |
| Custom directory | Specify the output directory. | |
| 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 |
| custom-dir | Custom directory | string |
| 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 |