BIPackage Pipelines CLI¶
Usage
bipipe [command] **params ...
Positional Arguments
| Command | Description |
|---|---|
bwa_dedup |
Run the bwa_dedup_sp_qc_mosdepth pipeline. |
gatk_gcnv |
Run the GATK GCNV pipeline. |
cnv_pon |
Run the Panel of Normals (PON) pipeline. |
snv_indel |
Run the SNV/Indel pipeline. |
cnv |
Run the CNV pipeline. |
get-config |
Get examples pipeline configurations in json format. |
Options
| Option | Description |
|---|---|
-h, --help |
Show this help message and exit |
--version |
Show program's version |