Man page - cnvkit-reference(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_REFERENCE
NAMEDESCRIPTION
positional arguments:
options:
To construct a generic, flat" copy number reference with neutral expectedcoverage:"
To disable specific automatic bias corrections:
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 expectedcoverage:"
-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.