cnvkit_segment - Infer copy number segments from the given
coverage table.
usage: cnvkit segment [-h] [-o FILENAME] [-d DATAFRAME]
- [-m {cbs,flasso,haar,none,hmm,hmm-tumor,hmm-germline}]
- [-t THRESHOLD] [--drop-low-coverage] [--drop-outliers FACTOR]
[--rscript-path PATH] [-p [PROCESSES]] [--smooth-cbs] [-v FILENAME] [-i
SAMPLE_ID] [-n NORMAL_ID] [--min-variant-depth MIN_VARIANT_DEPTH] [-z
[ALT_FREQ]] filename
- filename
- Bin-level log2 ratios (.cnr file), as produced by 'fix'.
- -h, --help
- show this help message and exit
- -o FILENAME, --output
FILENAME
- Output table file name (CNR-like table of segments, .cns).
- -d DATAFRAME,
--dataframe DATAFRAME
- File name to save the raw R dataframe emitted by CBS or Fused Lasso.
(Useful for debugging.)
- -m
{cbs,flasso,haar,none,hmm,hmm-tumor,hmm-germline}, --method
{cbs,flasso,haar,none,hmm,hmm-tumor,hmm-germline}
- Segmentation method (see docs), or 'none' for chromosome arm-level
averages as segments. [Default: cbs]
- -t THRESHOLD,
--threshold THRESHOLD
- Significance threshold (p-value or FDR, depending on method) to accept
breakpoints during segmentation. For HMM methods, this is the smoothing
window size.
- --drop-low-coverage
- Drop very-low-coverage bins before segmentation to avoid false-positive
deletions in poor-quality tumor samples.
- --drop-outliers
FACTOR
- Drop outlier bins more than this many multiples of the 95th quantile away
from the average within a rolling window. Set to 0 for no outlier
filtering. [Default: 10]
- --rscript-path
PATH
- Path to the Rscript executable to use for running R code. Use this option
to specify a non-default R installation. [Default: Rscript]
- -p [PROCESSES],
--processes [PROCESSES]
- Number of subprocesses to segment in parallel. Give 0 or a negative value
to use the maximum number of available CPUs. [Default: use 1 process]
- --smooth-cbs
- Perform an additional smoothing before CBS segmentation, which in some
cases may increase the sensitivity. Used only for CBS method.