NAME

       cnvkit_call - Call copy number variants from segmented log2 ratios.

DESCRIPTION

       usage: cnvkit 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).

   optional arguments:
       -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]