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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.












–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.

Read more here: Source link

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