Changes chromosome notation for each variant from the input, VCF or other variation files.
Element type: rename-chromosome-in-variation
Parameters
| Parameter | Description | Default value | Parameter in Workflow File | Type |
|---|---|---|---|---|
| Replace prefixes | Input the list of chromosome prefixes that you would like to replace. For example "NC_000". Separate different prefixes by semicolons. | prefixes-to-replace | string | |
| Replace by | Input the prefix that should be set instead, for example "chr". | prefix-replace-with | string |
Input/Output Ports
The element has 1 input ports:
Name in GUI: Input file URL
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 URL
Name in Workflow File: out-file
Slots:
| Slot In GUI | Slot in Workflow File | Type |
|---|---|---|
| Produced URL | url | string |