---
name: "cnvkit-genemetrics"
section: "1"
platform: "linux"
package: "cnvkit"
version: "0.9.12-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/cnvkit-genemetrics"
---

# cnvkit-genemetrics(1)

Identify targeted genes with copy number gain or loss.

## NAME

cnvkit\_genemetrics - Identify targeted genes with copy number gain or loss.

## DESCRIPTION

usage: cnvkit.py 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:

- filename

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

### options:

- **-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-ratio (unweighted).

- **--median**

  Median.

- **--mode**

  Mode (i.e. peak density of log2 ratios).

- **--ttest**

  One-sample t-test of bin log2 ratios versus 0.0.

- **--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**. \[Default: 100\]