.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.10.
.TH CNVKIT_METRICS "1" "March 2019" "cnvkit_metrics 0.9.5" "User Commands"
.SH NAME
cnvkit_metrics \- Compute coverage deviations and other metrics for self-evaluation.
.SH DESCRIPTION
usage: cnvkit metrics [\-h] [\-s SEGMENTS [SEGMENTS ...]] [\-\-drop\-low\-coverage]
.TP
[\-o FILENAME]
cnarrays [cnarrays ...]
.SS "positional arguments:"
.TP
cnarrays
One or more bin\-level coverage data files (*.cnn,
*.cnr).
.SS "optional arguments:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-s\fR SEGMENTS [SEGMENTS ...], \fB\-\-segments\fR 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.
.TP
\fB\-\-drop\-low\-coverage\fR
Drop very\-low\-coverage bins before calculations to
reduce negative "fat tail" of bin log2 values in poorquality tumor samples.
.TP
\fB\-o\fR FILENAME, \fB\-\-output\fR FILENAME
Output table file name.