Target Counts Options

The following options control the generation of target counts.

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--cnv-counts-method—Specifies the counting method for an alignment to be counted in a target bin. Values are midpoint, start, or overlap. The default value is overlap when using the panel of normal approach, which means if an alignment overlaps any part of the target bin, it is counted for that bin. In the self normalization mode, the default counting method is start.

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--cnv-min-mapq—Specifies the minimum MAPQ for an alignment to be counted during target counts generation. The default value is 3 for self normalization and 20 otherwise. When generating counts for panel of normals, all MAPQ0 alignments are counted.

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--cnv-target-bed—Specifies a properly formatted BED file that indicates the target intervals to sample coverage over. For use in WES analysis.

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--cnv-interval-width—Specifies the width of the sampling interval for CNV processing. This option controls the effective window size. The default is 1000 for WGS analysis and 500 for WES analysis.

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--cnv-skip-contig-list—Specifies a comma-separated list of contig identifiers to skip when generating intervals for WGS analysis. The default contigs that are skipped, if not specified, are "chrM,MT,m,chrm".