This section provides information on all the DRAGEN command-line options, including the name used in the configuration file, the command-line equivalent, a description, and the range of values.
NOTE After upgrading to a new version of DRAGEN, it is recommended to first run with the default DRAGEN options, including all filtering options, and then add any specific filters only if needed.
The following options are in the default section of the configuration file. The default section is at the top of the configuration file and does not have a section name (eg, [Aligner]) associated with it. Some mandatory fields must be specified on the command line and are not present in configuration files.
The following options are in the [Mapper] section of the configuration file. For more detailed information on these options, see [DNA Mapping]{.underline}.
The following options are in the [Aligner] section of the configuration file. For more information, see [DNA Aligning]{.underline}
If you disable automatic detection of insert-length statistics via the --enable-sampling option, you must override all the following options to specify the statistics. For more information, see [Mean Insert Size Detection]{.underline}. These options are part of the [Aligner] section of the configuration file.
The following options are in the Variant Caller section of the configuration file. For more information on these options, see [Variant Caller Options]{.underline}.
The following options are applicable to the CNV caller.
The following options can be set in the RepeatGenotyping section of the configuration file or on the command line. For more information, see Repeat Expansion Detection with Expansion Hunter [on page 1]{.underline}.
The following options are applicable to create the systematic noise BED file from normal VCFs.
Step 1. Run DRAGEN somatic tumor-only pipeline on each of approximately 50 normal samples.
Step 2. Generate the final noise file with:
There are three separate Explify capabilities available: the Explify analysis pipleine ("explify" prefix), a generalized metagenomics kmer classifier ("kmer-classifier" prefix), and a tool to build databases to be used by the kmer classifier ("kmer-class-db-builder" prefix).
¹ For exome or enrichment analysis, the default targeted callers are still enabled with the small variant caller, but will not generate any output.