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| CNVKIT_METRICS(1) |
User Commands |
CNVKIT_METRICS(1) |
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).
optional arguments:¶
- -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.
