NAME

       cnvkit_batch - Run the complete CNVkit pipeline on one or more BAM files.

DESCRIPTION

       usage: cnvkit batch [-h] [-m {hybrid,amplicon,wgs}]

       [--segment-method {cbs,flasso,haar,none,hmm,hmm-tumor,hmm-germline}]
              [-y]  [-c]  [--drop-low-coverage] [-p [PROCESSES]] [--rscript-path PATH] [-n [FILES
              ...]]  [-f  FILENAME]   [-t   FILENAME]   [-a   FILENAME]   [--annotate   FILENAME]
              [--short-names]      [--target-avg-size      TARGET_AVG_SIZE]     [-g     FILENAME]
              [--antitarget-avg-size         ANTITARGET_AVG_SIZE]          [--antitarget-min-size
              ANTITARGET_MIN_SIZE]  [--output-reference  FILENAME] [--cluster] [-r REFERENCE] [-d
              DIRECTORY] [--scatter] [--diagram] [bam_files ...]

   positional arguments:
       bam_files
              Mapped sequence reads (.bam)

   optional arguments:
       -h, --help
              show this help message and exit

       -m      {hybrid,amplicon,wgs},      --seq-method      {hybrid,amplicon,wgs},      --method
       {hybrid,amplicon,wgs}
              Sequencing   assay   type:  hybridization  capture  ('hybrid'),  targeted  amplicon
              sequencing ('amplicon'), or whole genome sequencing ('wgs'). Determines whether and
              how to use antitarget bins. [Default: hybrid]

       --segment-method {cbs,flasso,haar,none,hmm,hmm-tumor,hmm-germline}
              Method used in the 'segment' step. [Default: cbs]

       -y, --male-reference, --haploid-x-reference
              Use  or  assume a male reference (i.e. female samples will have +1 log-CNR of chrX;
              otherwise male samples would have -1 chrX).

       -c, --count-reads
              Get read depths by  counting  read  midpoints  within  each  bin.  (An  alternative
              algorithm).

       --drop-low-coverage
              Drop  very-low-coverage  bins before segmentation to avoid false-positive deletions
              in poor-quality tumor samples.

       -p [PROCESSES], --processes [PROCESSES]
              Number of subprocesses used to running each of the BAM files in  parallel.  Without
              an  argument,  use the maximum number of available CPUs. [Default: process each BAM
              in serial]

       --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]

   To construct a new copy number reference:
       -n [FILES ...], --normal [FILES ...]
              Normal  samples  (.bam) used to construct the pooled, paired, or flat reference. If
              this option is used but no filenames are given, a "flat" reference will  be  built.
              Otherwise, all filenames following this option will be used.

       -f FILENAME, --fasta FILENAME
              Reference genome, FASTA format (e.g. UCSC hg19.fa)

       -t FILENAME, --targets FILENAME
              Target intervals (.bed or .list)

       -a FILENAME, --antitargets FILENAME
              Antitarget intervals (.bed or .list)

       --annotate FILENAME
              Use  gene models from this file to assign names to the target regions. Format: UCSC
              refFlat.txt or ensFlat.txt  file  (preferred),  or  BED,  interval  list,  GFF,  or
              similar.

       --short-names
              Reduce multi-accession bait labels to be short and consistent.

       --target-avg-size TARGET_AVG_SIZE
              Average size of split target bins (results are approximate).

       -g FILENAME, --access FILENAME
              Regions  of  accessible  sequence  on chromosomes (.bed), as output by the 'access'
              command.

       --antitarget-avg-size ANTITARGET_AVG_SIZE
              Average size of antitarget bins (results are approximate).

       --antitarget-min-size ANTITARGET_MIN_SIZE
              Minimum size of antitarget bins (smaller regions are dropped).

       --output-reference FILENAME
              Output filename/path for the new reference file being created. (If  given,  ignores
              the  -o/--output-dir  option  and will write the file to the given path. Otherwise,
              "reference.cnn" will be created  in  the  current  directory  or  specified  output
              directory.)

       --cluster
              Calculate and use cluster-specific summary stats in the reference pool to normalize
              samples.

   To reuse an existing reference:
       -r REFERENCE, --reference REFERENCE
              Copy number reference file (.cnn).

   Output options:
       -d DIRECTORY, --output-dir DIRECTORY
              Output directory.

       --scatter
              Create a whole-genome copy ratio profile as a PDF scatter plot.

       --diagram
              Create an ideogram of copy ratios on chromosomes as a PDF.