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]