Command-Line Options

The following command line options are supported for the Structural Variant Caller.

The DRAGEN SV pipeline shares the following input and output options with the DRAGEN Host Software. You can use BAM and CRAM files as input. Alternatively, if using read mapping with the SV calling in a single run, you can use all of the DRAGEN input options, including FASTQ, BAM, and CRAM files.

Option

Description

--bam-input

The BAM file to be processed.

--tumor-bam-input

If performing tumor-normal or tumor-only analysis, the tumor BAM file to be processed.

--cram-input

The CRAM file to be processed.

--tumor-cram-input

If performing tumor-normal or tumor-only analysis, the tumor CRAM file to be processed.

--enable-map-align

Enables DRAGEN map/align. The default is true, so all input reads are remapped and aligned unless the option is set to false.

--fastq-file1, --fastq-file2, --fastq-list

Input FASTQ files or list of files to be processed.

--tumor-fastq1, --tumor-fastq2, --tumor-fastq-list

Input tumor FASTQ file or list of files to be processed.

--ref-dir

The DRAGEN reference genome hashtable directory. For more information about the reference genome hashtable, see Prepare a Reference Genome.

--output-directory

Output directory where all results are stored.

--output-file-prefix

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

Option

Description

--enable-sv

Enable or disable the structural variant caller. The default is false.

--sv-call-regions-bed

Specifies a BED file containing the set of regions to call. Optionally, you can compress the file in gzip or bgzip format.

--sv-exclusion-bed

Specifies a BED file containing the set of regions to exclude for the SV calling. Optionally, you can compress the file in gzip or bgzip format.

--sv-region

Limit the analysis to a specified region of the genome for debugging purposes. This option can be specified multiple times to build a list of regions. The value must be in the format “chr:startPos-endPos”.

--sv-exome

Set to true to configure the variant caller for targeted sequencing inputs, which includes disabling high depth filters. In integrated mode, the default is to autodetect targeted sequencing input, and in standalone mode the default is false.

--sv-output-contigs

Set to true to have assembled contig sequences output in a VCF file. The default is false.

--sv-forcegt-vcf

Specify a VCF of structural variants for forced genotyping. The variants are scored and emitted in the output VCF even if not found in the sample data. The variants are merged with any additional variants discovered directly from the sample data.

--sv-discovery

Enable SV discovery. This flag can be set to false only when --sv-forcegt-vcf is used. When set to false, SV discovery is disabled and only the forced genotyping input variants are processed. The default is true.

--sv-use-overlap-pair-evidence

Allow overlapping read pairs to be considered as evidence. By default, DRAGEN uses autodetect on the fraction of overlapping read pairs if <20%.

--sv-somatic-ins-tandup-hotspot-regions-bed

Specify a BED of ITD hotspot regions to increase sensitivity for calling ITDs in somatic variant analysis. By default, DRAGEN SV automatically selects areference-specific hotspots BED file from /opt/edico/config/sv_somatic_ins_tandup_hotspot_*.bed.

--sv-enable-somatic-ins-tandup-hotspot-regions

Enable or disable the ITD hotspot region input. The default is true in somatic variant analysis.

--sv-enable-liquid-tumor-mode

Enable liquid tumor mode. See Liquid Tumor Calling for more information.

--sv-tin-contam-tolerance

Set the Tumor-in-Normal (TiN) contamination tolerance level. See Liquid Tumor Calling for more information.

--sv-systematic-noise

Systematic noise BEDPE file containing the set of noisy paired regions (optionally gzip or bzip compressed). For more information see Systematic Noise Filtering for more infprmation.