Structural Variant Calling Options

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

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--enable-sv—Enable or disable the structural variant caller. The default is false.

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--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.

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--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”.

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--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.

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

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--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.

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--sv-discovery—Flag to 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.