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

# cnvkit-import-picard(1)

Convert Picard CalculateHsMetrics tabular output to CNVkit .cnn files. The input file is generated by the PER\_TARGET\_COVERAGE option in the CalculateHsMetrics script in Picard tools. If 'antitarget' is in the input filename, the generated output filename will have the suffix '.antitargetcoverage.cnn', otherwise '.targetcoverage.cnn'.

## NAME

cnvkit\_import-picard - Convert Picard CalculateHsMetrics tabular output to CNVkit .cnn files.

    The input file is generated by the PER\_TARGET\_COVERAGE option in the\
     CalculateHsMetrics script in Picard tools.

    If 'antitarget' is in the input filename, the generated output filename will\
     have the suffix '.antitargetcoverage.cnn', otherwise '.targetcoverage.cnn'.

## DESCRIPTION

usage: cnvkit.py import-picard \[-h\] \[-d DIRECTORY\] targets \[targets ...\]

### positional arguments:

- targets

  Sample coverage .csv files (target and antitarget).

### options:

- **-h**, **--help**

  show this help message and exit

- **-d** DIRECTORY, **--output-dir** DIRECTORY

  Output directory name.