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CNVKIT_IMPORT-PICARD(1) User Commands CNVKIT_IMPORT-PICARD(1)

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 import-picard [-h] [-d DIRECTORY] targets [targets ...]

positional arguments:

targets
Sample coverage .csv files (target and antitarget).

optional arguments:

-h, --help
show this help message and exit
-d DIRECTORY, --output-dir DIRECTORY
Output directory name.
March 2019 cnvkit_import-picard 0.9.5