`kcftools splitKCF`¶

The splitKCF command in kcftools is used to split a single KCF file into per-chromosome files. This is especially useful when working with large genome-wide variation data and you need to analyze or visualize data one chromosome at a time.

Usage¶

$ kcftools splitKCF -k=<kcfFile> -o=<outDir>

Description¶

KCF (K-mer Comparison Format) files may contain genome-wide variation or similarity data. When working with such large-scale data, it is often necessary to analyze data chromosome by chromosome, or to parallelize processing by splitting the input per chromosome.

This command reads a full KCF file and generates a separate KCF file for each chromosome found in the original input. The split files are saved in the specified output directory, and named appropriately (usually including the chromosome name or number).

Options¶

Option	Description	Required
`-k`, `--kcf=<kcfFile>`	Input KCF file to be split	Yes
`-o`, `--output=<outDir>`	Output directory where files will be saved	Yes

Output¶

For each chromosome in the input KCF file, a new .kcf file will be created in the specified output directory. For example, if your input file contains data for chromosomes chr1, chr2, and chrX, the output directory will contain:

output_directory/
├── chr1.kcf
├── chr2.kcf
└── chrN.kcf

These files can then be used for chromosome-specific analysis, visualization, or downstream pipelines such as matrix conversion (kcfToMatrix), plotting, or region filtering.

Example¶

$ kcftools splitKCF -k merged_variations.kcf -o split_by_chrom/

This command will read merged_variations.kcf and generate one file per chromosome under the split_by_chrom/ directory.

Note

Ensure the input KCF file is correctly formatted and includes chromosome information per entry.
The output directory will be created if it does not already exist.
This is a utility command—useful before plotting, matrix generation, or when managing large data.

Help¶

To view help for this command:

$ kcftools splitKCF --help

kcftools splitKCF¶