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]] [--smooth-cbs] [-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 (see docs), 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]

       --smooth-cbs
              Perform an additional smoothing before CBS segmentation, which in  some  cases  may  increase  the
              sensitivity. Used only for CBS method.

   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]