Man page - cnvkit-segment(1)
Packages contains this manual
- cnvkit-import-theta(1)
- cnvkit-coverage(1)
- cnvkit-metrics(1)
- cnvkit-import-seg(1)
- cnvkit-export(1)
- cnvkit-breaks(1)
- cnvkit-fix(1)
- cnvkit-segmetrics(1)
- cnvkit-batch(1)
- cnvkit-import-rna(1)
- cnvkit-bintest(1)
- cnvkit-diagram(1)
- cnvkit-call(1)
- cnvkit-autobin(1)
- cnvkit-access(1)
- cnvkit-antitarget(1)
- cnvkit-sex(1)
- cnvkit-segment(1)
- cnvkit-genemetrics(1)
- cnvkit-heatmap(1)
- cnvkit-target(1)
- cnvkit-import-picard(1)
- cnvkit-reference(1)
- cnvkit-scatter(1)
apt-get install cnvkit
Manual
CNVKIT_SEGMENT
NAMEDESCRIPTION
positional arguments:
options:
To additionally segment SNP b-allele frequencies:
NAME
cnvkit_segment - Infer copy number segments from the given coverage table.
DESCRIPTION
usage: cnvkit.py
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
positional arguments:
filename
Bin-level log2 ratios (.cnr file), as produced by ’fix’.
options:
-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.
To additionally segment SNP b-allele frequencies:
-v FILENAME, --vcf FILENAME
VCF file name containing variants for segmentation by allele frequencies.
-i SAMPLE_ID, --sample-id SAMPLE_ID
Specify the name of the sample in the VCF ( -v /--vcf) to use for b-allele frequency extraction and as the default plot title.
-n NORMAL_ID, --normal-id NORMAL_ID
Corresponding normal sample ID in the input VCF ( -v /--vcf). This sample is used to select only germline SNVs to plot b-allele frequencies.
--min-variant-depth MIN_VARIANT_DEPTH
Minimum read depth for a SNV to be displayed in the b-allele frequency plot. [Default: 20]
-z [ALT_FREQ], --zygosity-freq [ALT_FREQ]
Ignore VCF’s genotypes (GT field) and instead infer zygosity from allele frequencies. [Default if used without a number: 0.25]