NAME

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

DESCRIPTION

       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]  [--stdev]
              [--sem] [--mad] [--mse] [--iqr] [--bivar] [--ci] [--pi] [-a ALPHA] [-b BOOTSTRAP] filename

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

   optional arguments:
       -h, --help
              show this help message and exit

       -s SEGMENT, --segment SEGMENT
              Segmentation calls (.cns), the output of the 'segment' command).

       -t THRESHOLD, --threshold THRESHOLD
              Copy number change threshold to report a gene gain/loss. [Default: 0.2]

       -m MIN_PROBES, --min-probes MIN_PROBES
              Minimum number of covered probes to report a gain/loss. [Default: 3]

       --drop-low-coverage
              Drop very-low-coverage bins before segmentation to avoid false-positive deletions in  poor-quality
              tumor samples.

       -y, --male-reference, --haploid-x-reference
              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).

       -x     {m,y,male,Male,f,x,female,Female},     --sample-sex     {m,y,male,Male,f,x,female,Female},      -g
       {m,y,male,Male,f,x,female,Female}, --gender {m,y,male,Male,f,x,female,Female}
              Specify the sample's chromosomal sex as male or female. (Otherwise guessed from X and Y coverage).

       -o FILENAME, --output FILENAME
              Output table file name.

   Statistics available:
       --mean Mean log2 value (unweighted).

       --median
              Median.

       --mode Mode (i.e. peak density of log2 values).

       --stdev
              Standard deviation.

       --sem  Standard error of the mean.

       --mad  Median absolute deviation (standardized).

       --mse  Mean squared error.

       --iqr  Inter-quartile range.

       --bivar
              Tukey's biweight midvariance.

       --ci   Confidence interval (by bootstrap).

       --pi   Prediction interval.

       -a ALPHA, --alpha ALPHA
              Level to estimate confidence and prediction intervals; use with --ci and --pi. [Default: 0.05]

       -b BOOTSTRAP, --bootstrap BOOTSTRAP
              Number of bootstrap iterations to estimate confidence interval; use with --ci. [Default: 100]