Output and Filtering Options

The output and filtering options control the CNV output files.

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--cnv-blacklist-bed—Specifies a BED file indicating intervals to exclude from the from CNV analysis. If a target interval overlaps regions specified from blacklist BED file more thancnv-blacklist-min-overlap, it is suppressed.

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--cnv-blacklist-min-overlap—Specifies a fraction for filtering threshold of overlap amount between target interval and blacklist region (0.5).

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--cnv-enable-plots—Generate plots as part of the CNV pipeline. The default is false.

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If you perform WGS CNV analysis with high-resolution intervals (less than 1000 bp), then plot generation can take longer to complete. Illumina recommends that you use the default (disabled).

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--cnv-enable-ref-calls—Emit copy neutral (REF) calls in the output VCF file. The default is true for single WGS CNV analysis.

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--cnv-enable-tracks—Generate track files that can be imported into IGV for viewing. When this option is enabled, a *.gff file for the output variant calls is generated, as well as *.bw files for the tangent normalized signal. The default is true.

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--cnv-filter-bin-support-ratio—Filters out a candidate event if the span of supporting bins is less than the specified ratio with respect to the overall event length. The default ratio is 0.2 (20% support). As an example, if an event is called and has a length of 100,000 bp, but the target interval bins that support the call only spans a total of 15,000 bp (15,000/100,000 = 0.15), then it will be filtered out.

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--cnv-filter-copy-ratio—Specifies the minimum copy ratio threshold value centered about 1.0 at which a reported event is marked as PASS in the output VCF file. The default value is 0.2, leading to calls less than CR=0.8 or greater than CR=1.2.

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--cnv-filter-length—Specifies the minimum event length in bases at which a reported event is marked as PASS in the output VCF file. The default is 10000.

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--cnv-filter-qual—Specifies the QUAL value at which a reported event is marked as PASS in the output VCF file. The default is 10.

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--cnv-min-qual—Specifies the minimum reported QUAL. The default is 3.

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--cnv-max-qual—Specifies the maximum reported QUAL. The default is 200.

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--cnv-ploidy—Specifies the normal ploidy value. This option is used only for estimation of the copy number value emitted in the output VCF file. The default is 2.

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--cnv-qual-length-scale—Specifies the bias weighting factor to adjust QUAL estimates for segments with longer lengths. This is an advanced option and should not need to be modified. The default is 0.9303 (2-0.1).

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--cnv-qual-noise-scale—Specifies the bias weighting factor to adjust QUAL estimates based on sample variance. This is an advanced option and should not need to be modified. The default is 1.0.