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.