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| CNVKIT_IMPORT-SEG(1) |
User Commands |
CNVKIT_IMPORT-SEG(1) |
NAME¶
cnvkit_import-seg - Convert a SEG file to CNVkit .cns files.
DESCRIPTION¶
usage: cnvkit import-seg [-h] [-c CHROMOSOMES] [-p PREFIX] [--from-log10]
- [-d DIRECTORY]
- segfile
positional arguments:¶
- segfile
- Input file in SEG format. May contain multiple samples.
optional arguments:¶
- -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.
