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cnvkit_genemetrics - Identify targeted genes with copy number gain or loss.


usage: cnvkit genemetrics [-h] [-s SEGMENT] [-t THRESHOLD] [-m MIN_PROBES]

[--drop-low-coverage] [-y]
[-x {m,y,male,Male,f,x,female,Female}] [-o FILENAME] [--mean] [--median] [--mode] [--ttest] [--stdev] [--sem] [--mad] [--mse] [--iqr] [--bivar] [--ci] [--pi] [-a ALPHA] [-b BOOTSTRAP] filename

positional arguments:

Processed sample coverage data file (*.cnr), the output of the 'fix' sub-command.


show this help message and exit
Segmentation calls (.cns), the output of the 'segment' command).
Copy number change threshold to report a gene gain/loss. [Default: 0.2]
Minimum number of covered probes to report a gain/loss. [Default: 3]
Drop very-low-coverage bins before segmentation to avoid false-positive deletions in poor-quality tumor samples.
Assume inputs were normalized to a male reference (i.e. female samples will have +1 log-coverage of chrX; otherwise male samples would have -1 chrX).
Specify the sample's chromosomal sex as male or female. (Otherwise guessed from X and Y coverage).
Output table file name.

Statistics available:

Mean log2-ratio (unweighted).
Mode (i.e. peak density of log2 ratios).
One-sample t-test of bin log2 ratios versus 0.0.
Standard deviation.
Standard error of the mean.
Median absolute deviation (standardized).
Mean squared error.
Inter-quartile range.
Tukey's biweight midvariance.
Confidence interval (by bootstrap).
Prediction interval.
Level to estimate confidence and prediction intervals; use with --ci and --pi. [Default: 0.05]
Number of bootstrap iterations to estimate confidence interval; use with --ci. [Default: 100]
September 2022 cnvkit genemetrics 0.9.9