NAME
cnvkit_import-seg - Convert a SEG file to CNVkit .cns files.
DESCRIPTION
usage: cnvkit.py import-seg [-h] [-c CHROMOSOMES] [-p PREFIX] [--from-log10]
- [-d DIRECTORY]
-
segfile
positional arguments:
- segfile
-
Input file in SEG format. May contain multiple samples.
options:
- -h, --help
-
show this help message and exit
- -c CHROMOSOMES, --chromosomes CHROMOSOMES
-
Mapping of chromosome indexes to names. Syntax: "from1:to1,from2:to2". Or use "human" for the preset: "23:X,24:Y,25:M".
- -p PREFIX, --prefix PREFIX
-
Prefix to add to chromosome names (e.g 'chr' to rename '8' in the SEG file to 'chr8' in the output).
- --from-log10
-
Convert base-10 logarithm values in the input to base-2 logs.
- -d DIRECTORY, --output-dir DIRECTORY
-
Output directory name.