Structural Variant Caller Options

enable-sv

Enable/disable structural variant caller. Default is false.

--enable-sv

sv-call-regions-bed

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

--sv-call-regions-bed

sv-denovo-scoring

Enable/disable de novo quality scoring for for structural variant joint diploid calling. Pedigree file must also be provided.

--sv-denovo-scoring

sv-forcegt-vcf

Specify a VCF of structural variants for forced genotyping. The variants are scored and included 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-forcegt-vcf

sv-discovery

Enable SV discovery. This flag can be set to false when using --sv-forcegt-vcf to indicate that SV discovery should be disabled and only the forced genotyping input should be used.

--sv-discovery

sv-exome

When set to true, configures the variant caller for targeted sequencing inputs, which includes disabling high depth filters. Default is false.

--sv-exome

sv-output-contigs

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

--sv-output-contigs