CNVKIT_METRICS

NAME

cnvkit_metrics - Compute coverage deviations and other metrics for self-evaluation.

DESCRIPTION

usage: cnvkit metrics [-h] [-s SEGMENTS [SEGMENTS ...]] [--drop-low-coverage]
[-o FILENAME]

cnarrays [cnarrays ...]

positional arguments:

cnarrays

One or more bin-level coverage data files (*.cnn, *.cnr).

options:

-h, --help

show this help message and exit

-s SEGMENTS [SEGMENTS ...], --segments SEGMENTS [SEGMENTS ...]

One or more segmentation data files (*.cns, output of the ’segment’ command). If more than one file is given, the number must match the coverage data files, in which case the input files will be paired together in the given order. Otherwise, the same segments will be used for all coverage files.

--drop-low-coverage

Drop very-low-coverage bins before calculations to reduce negative "fat tail" of bin log2 values in poorquality tumor samples.

-o FILENAME, --output FILENAME

Output table file name.