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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.


The BAM file to be processed.


The CRAM file to be processed.


Enable or disable CNV processing. Set to true to enable CNV processing.


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 file or files to be processed.


Output directory where all results are stored.


Output file prefix that will be prepended to all result file names.


The DRAGEN reference genome hashtable directory.

Read more here: Source link

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