Welcome to KCFtools Documentation!¶

KCFtools is a Java-based toolset for identifying genomic variations through counting kmer presence/absence between reference and query genomes. It utilizes precomputed k-mer count databases (from KMC) to perform a wide array of genomic analyses including variant detection, IBS window identification, and genotype matrix generation.

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License¶

This project is licensed under the GNU General Public License v3.0 only (GPL-3.0-only).

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Contents¶

General Information¶

• Quick Start
• Installation
• Workflow
• Features
• Methodology

Usage¶

• Command Line Interface
• getVariations
• cohort
• findIBS
• splitKCF
• getAttributes
• kcf2gt
• kcf2tsv
• increaseWindow
• scoreRecalc
• kcf2plink

File Formats¶

• KCF File
• KMC Database
• Genotype Table File
• Attributes File
• IBS Summary File

Additional Information¶