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| CNVKIT_BATCH(1) |
User Commands |
CNVKIT_BATCH(1) |
NAME¶
cnvkit_batch - Run the complete CNVkit pipeline on one or more BAM files.
DESCRIPTION¶
usage: cnvkit batch [-h] [-m {hybrid,amplicon,wgs}] [-y] [-c]
- [--drop-low-coverage] [-p [PROCESSES]]
- [--rscript-path PATH] [-n [FILES [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]
[-r REFERENCE] [-d DIRECTORY] [--scatter] [--diagram] [bam_files
[bam_files ...]]
positional arguments:¶
- bam_files
- Mapped sequence reads (.bam)
optional arguments:¶
- -h, --help
- show this help message and exit
- -m {hybrid,amplicon,wgs}, --method
{hybrid,amplicon,wgs}
- Sequencing protocol: hybridization capture ('hybrid'), targeted amplicon
sequencing ('amplicon'), or whole genome sequencing ('wgs'). Determines
whether and how to use antitarget bins. [Default: hybrid]
- -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 [FILES ...]], --normal [FILES [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.)
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.
