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]