cnvkit_reference - Compile a coverage reference from the given
files (normal samples).
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 ...]
- references
- Normal-sample target or antitarget .cnn files, or the directory that
contains them.
- -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.