Man page - cnvkit-batch(1)
Packages contains this manual
- cnvkit-import-theta(1)
- cnvkit-coverage(1)
- cnvkit-metrics(1)
- cnvkit-import-seg(1)
- cnvkit-export(1)
- cnvkit-breaks(1)
- cnvkit-fix(1)
- cnvkit-segmetrics(1)
- cnvkit-batch(1)
- cnvkit-import-rna(1)
- cnvkit-bintest(1)
- cnvkit-diagram(1)
- cnvkit-call(1)
- cnvkit-autobin(1)
- cnvkit-access(1)
- cnvkit-antitarget(1)
- cnvkit-sex(1)
- cnvkit-segment(1)
- cnvkit-genemetrics(1)
- cnvkit-heatmap(1)
- cnvkit-target(1)
- cnvkit-import-picard(1)
- cnvkit-reference(1)
- cnvkit-scatter(1)
apt-get install cnvkit
Manual
CNVKIT_BATCH
NAMEDESCRIPTION
positional arguments:
options:
To construct a new copy number reference:
To reuse an existing reference:
Output options:
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.