DOKK / manpages / debian 10 / cnvkit / cnvkit-reference.1.en

cnvkit_reference - Compile a coverage reference from the given files (normal samples).

usage: cnvkit reference [-h] [-f FASTA] [-o FILENAME] [-y]

[-x {m,y,male,Male,f,x,female,Female}] [-t TARGETS]
[-a ANTITARGETS] [--no-gc] [--no-edge] [--no-rmask] [references [references ...]]

Normal-sample target or antitarget .cnn files, or the directory that contains them.

show this help message and exit
Reference genome, FASTA format (e.g. UCSC hg19.fa)
Output file name.
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.
Specify the chromosomal sex of all given samples as male or female. (Default: guess each sample from coverage of X and Y chromosomes).

Target intervals (.bed or .list)
Antitarget intervals (.bed or .list)

Skip GC correction.
Skip edge-effect correction.
Skip RepeatMasker correction.
March 2019 cnvkit_reference 0.9.5