Man page - cnvkit-reference(1)
Packages contas this manual
- cnvkit-import-seg(1)
- cnvkit-breaks(1)
- cnvkit-heatmap(1)
- cnvkit-import-theta(1)
- cnvkit-autobin(1)
- cnvkit-sex(1)
- cnvkit-diagram(1)
- cnvkit-reference(1)
- cnvkit-genemetrics(1)
- cnvkit-segment(1)
- cnvkit-scatter(1)
- cnvkit-target(1)
- cnvkit-call(1)
- cnvkit-batch(1)
- cnvkit-metrics(1)
- cnvkit-segmetrics(1)
- cnvkit-coverage(1)
- cnvkit-export(1)
- cnvkit-import-picard(1)
- cnvkit-fix(1)
- cnvkit-bintest(1)
- cnvkit-import-rna(1)
- cnvkit-antitarget(1)
- cnvkit-access(1)
Package: cnvkit
apt-get install cnvkit
apt-get install cnvkit
Manuals in package:
Documentations in package:
Manual
| CNVKIT_REFERENCE(1) | User Commands | CNVKIT_REFERENCE(1) |
NAME
cnvkit_reference - Compile a coverage reference from the given files (normal samples).
DESCRIPTION
usage: cnvkit.py reference [-h] [-f FASTA] [-o FILENAME] [-c]
- [--min-cluster-size NUM]
- [-x {m,y,male,Male,f,x,female,Female}] [-y] [-t TARGETS] [-a ANTITARGETS] [--no-gc] [--no-edge] [--no-rmask] [references ...]
positional arguments:
- references
- Normal-sample target or antitarget .cnn files, or the directory that contains them.
options:
- -h, --help
- show this help message and exit
- -f FASTA, --fasta FASTA
- Reference genome, FASTA format (e.g. UCSC hg19.fa)
- -o FILENAME, --output FILENAME
- Output file name.
- -c, --cluster
- Calculate and store summary stats for clustered subsets of the normal samples with similar coverage profiles.
- --min-cluster-size NUM
- Minimum cluster size to keep in reference profiles. [Default: 4]
- -x {m,y,male,Male,f,x,female,Female}, --sample-sex {m,y,male,Male,f,x,female,Female}, -g {m,y,male,Male,f,x,female,Female}, --gender {m,y,male,Male,f,x,female,Female}
- Specify the chromosomal sex of all given samples as male or female. (Default: guess each sample from coverage of X and Y chromosomes).
- -y, --male-reference, --haploid-x-reference
- Create a male reference: shift female samples' chrX log-coverage by -1, so the reference chrX average is -1. Otherwise, shift male samples' chrX by +1, so the reference chrX average is 0.
To construct a generic, flat" copy number reference with neutral expected coverage:"
- -t TARGETS, --targets TARGETS
- Target intervals (.bed or .list)
- -a ANTITARGETS, --antitargets ANTITARGETS
- Antitarget intervals (.bed or .list)
To disable specific automatic bias corrections:
- --no-gc
- Skip GC correction.
- --no-edge
- Skip edge-effect correction.
- --no-rmask
- Skip RepeatMasker correction.
| July 2023 | cnvkit.py reference 0.9.10 |