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
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The BAM file to be processed.
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–cram-input
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The CRAM file to be processed.
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–enable-cnv
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Enable or disable CNV processing. Set to true to enable CNV processing.
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–enable-map-align
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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.
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–fastq-file1
–fastq-file2
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FASTQ file or files to be processed.
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–output-directory
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Output directory where all results are stored.
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–output-file-prefix
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Output file prefix that will be prepended to all result file names.
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–ref-dir
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The DRAGEN reference genome hashtable directory.
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