Man page - cnvkit-call(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_CALL
NAMEDESCRIPTION
positional arguments:
options:
To additionally process SNP b-allele frequencies for allelic copy number:
NAME
cnvkit_call - Call copy number variants from segmented log2 ratios.
DESCRIPTION
usage: cnvkit.py
call [-h] [--center [{mean,median,mode,biweight}]]
[--center-at CENTER_AT] [--filter {ampdel,cn,ci,sem}]
[-m {threshold,clonal,none}] [-t THRESHOLDS] [--ploidy PLOIDY] [--purity PURITY] [--drop-low-coverage] [-x {m,y,male,Male,f,x,female,Female}] [-y] [-o FILENAME] [-v FILENAME] [-i SAMPLE_ID] [-n NORMAL_ID] [--min-variant-depth MIN_VARIANT_DEPTH] [-z [ALT_FREQ]] filename
positional arguments:
filename
Copy ratios (.cnr or .cns).
options:
-h , --help
show this help message and exit
--center [{mean,median,mode,biweight}]
Re-center the log2 ratio values using this estimator of the center or average value. (’median’ if no argument given.)
--center-at CENTER_AT
Subtract a constant number from all log2 ratios. For "manual" re-centering, in case the --center option gives unsatisfactory results.)
--filter {ampdel,cn,ci,sem}
Merge segments flagged by the specified filter(s) with the adjacent segment(s).
-m {threshold,clonal,none}, --method {threshold,clonal,none}
Calling method. [Default: threshold]
-t THRESHOLDS, --thresholds THRESHOLDS
Hard thresholds for calling each integer copy number, separated by commas. Use the ’=’ sign on the command line, e.g.: -t = -1 ,0,1 [Default: -1 .1,-0.25,0.2,0.7]
--ploidy PLOIDY
Ploidy of the sample cells. [Default: 2]
--purity PURITY
Estimated tumor cell fraction, a.k.a. purity or cellularity.
--drop-low-coverage
Drop very-low-coverage bins before segmentation to avoid false-positive deletions in poor-quality tumor samples.
-x
{m,y,male,Male,f,x,female,Female},
--sample-sex
{m,y,male,Male,f,x,female,Female},
-g
{m,y,male,Male,f,x,female,Female},
--gender
{m,y,male,Male,f,x,female,Female}
Specify the sample’s chromosomal sex as male or female. (Otherwise guessed from X and Y coverage).
-y , --male-reference , --haploid-x-reference
Was a male reference used? If so, expect half ploidy on chrX and chrY; otherwise, only chrY has half ploidy. In CNVkit, if a male reference was used, the "neutral" copy number (ploidy) of chrX is 1; chrY is haploid for either reference sex.
-o FILENAME, --output FILENAME
Output table file name (CNR-like table of segments, .cns).
To additionally process SNP b-allele frequencies for allelic copy number:
-v FILENAME, --vcf FILENAME
VCF file name containing variants for calculation of b-allele frequencies.
-i SAMPLE_ID, --sample-id SAMPLE_ID
Name of the sample in the VCF ( -v /--vcf) to use for b-allele frequency extraction.
-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 calculate b-allele frequencies.
--min-variant-depth MIN_VARIANT_DEPTH
Minimum read depth for a SNV to be used in the b-allele frequency calculation. [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]