CNV Pipeline Options
The following are the top-level options that are shared with the DRAGEN Host Software to control the CNV pipeline. You can input a BAM or CRAM file into the CNV pipeline. If you are using the DRAGEN mapper and aligner, you can use FASTQ files.
|
Option |
Description |
|---|---|
|
--bam-input |
The BAM file to be processed. |
|
--cram-input |
The CRAM file to be processed. |
|
--enable-cnv |
Enable or disable CNV processing. Set to true to enable CNV processing. |
|
--enable-map-align |
Enables the mapper and aligner module. The default is true, so all input reads are remapped and aligned unless this option is set to false. |
|
--fastq-file1 --fastq-file2 |
FASTQ file or files to be processed. |
|
--output-directory |
Output directory where all results are stored. |
|
--output-file-prefix |
Output file prefix that will be prepended to all result file names. |
|
--ref-dir |
The DRAGEN reference genome hashtable directory. |
