kcftools Command Line Interface¶

kcftools provides a suite of tools to handle k-mer counting based variation analysis.

Usage¶

$ kcftools [-hV] [COMMAND]

Options¶

• -h, --help : Show this help message and exit.
• -V, --version : Print version information and exit.

Available Commands¶

getVariations¶

Screen for reference kmers that are not present in the KMC database, and detect variation.

$ kcftools getVariations [OPTIONS]

cohort¶

Create a cohort of sample KCF files.

$ kcftools cohort [OPTIONS]

findIBS¶

Find Identity-By-State (IBS) windows in a KCF file.

$ kcftools findIBS [OPTIONS]

splitKCF¶

Split a KCF file by chromosome.

$ kcftools splitKCF [OPTIONS]

getAttributes¶

Extract attributes from KCF files.

$ kcftools getAttributes [OPTIONS]

kcfToMatrix¶

Convert KCF windows into a genotype matrix.

$ kcftools kcfToMatrix [OPTIONS]

kcf2tsv¶

Convert a KCF file into a TSV file (similar to IBSpy output).

$ kcftools kcf2tsv [OPTIONS]

increaseWindow¶

Increase the window size of a KCF file by merging windows.

$ kcftools increaseWindow [OPTIONS]

For detailed help on a specific command, run:

$ kcftools <COMMAND> --help