cnvkit-reference(1)

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.