table of contents
| CNVKIT_REFERENCE(1) | User Commands | CNVKIT_REFERENCE(1) |
NAME¶
cnvkit_reference - Compile a coverage reference from the given files (normal samples).
DESCRIPTION¶
usage: cnvkit 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.
optional arguments:¶
- -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.
- -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.
| October 2021 | cnvkit reference 0.9.9 |