Circular Binary Segmentation

Circular Binary Segmentation is implemented directly in DRAGEN and is based on A faster circular binary segmentation for the analysis of array CGH data with enhancements to improve sensitivity for NGS data.

The following options control Circular Binary Segmentation.

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--c-alpha—Specifies the significance level for the test to accept change points. The default is 0.01.

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--cnv-cbs-eta—Specifies the Type I error rate of the sequential boundary for early stopping when using the permutation method. The default is 0.05.

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--cnv-cbs-kmax—Specifies maximum width of smaller segment for permutation. The default is 25.

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--cnv-cbs-min-width—Specifies the minimum number of markers for a changed segment. The default is 2.

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--cnv-cbs-nmin—Specifies the minimum length of data for maximum statistic approximation. The default is 200.

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--cnv-cbs-nperm—Specifies the number of permutations used for p-value computation. The default is 10000.

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--cnv-cbs-trim—Specifies the proportion of data to be trimmed for variance calculations. The default is 0.025.