---
name: "cnvkit-batch"
section: "1"
platform: "linux"
package: "cnvkit"
version: "0.9.12-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/cnvkit-batch"
---

# cnvkit-batch(1)

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

## NAME

cnvkit\_batch - Run the complete CNVkit pipeline on one or more BAM files.

## DESCRIPTION

usage: cnvkit.py 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)

### options:

- **-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.