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| CNVKIT_SEGMENT(1) |
User Commands |
CNVKIT_SEGMENT(1) |
NAME¶
cnvkit_segment - Infer copy number segments from the given coverage table.
DESCRIPTION¶
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]] [-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'.
optional arguments:¶
- -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 (CBS, fused lasso, haar wavelet, HMM), 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]
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]
