KCF File Format¶

The Kmer Count Format (.kcf) file summarizes the variation profile of a query relative to a reference genome using k-mer presence/absence matrices.

KCF File Header Description¶

The .kcf file begins with a series of metadata headers describing the format version, reference genome, software used, and analysis parameters.

Example Header Lines¶

##format=KCF0.1
##date=2024-12-05
##source=kcftools
##reference=lsatv11.chr3.fasta
##contig=<ID=chr3,length=324658466>
##INFO=<ID=IS,Type=Float,Description="Minimum score for the window">
##INFO=<ID=XS,Type=Float,Description="Maximum score for the window">
##INFO=<ID=MS,Type=Float,Description="Mean score for the window">
##INFO=<ID=IO,Type=Integer,Description="Minimum observed kmers in the window">
##INFO=<ID=XO,Type=Integer,Description="Maximum observed kmers in the window">
##INFO=<ID=MO,Type=Integer,Description="Mean observed kmers in the window">
##INFO=<ID=IV,Type=Integer,Description="Minimum variations in the window">
##INFO=<ID=XV,Type=Integer,Description="Maximum variations in the window">
##INFO=<ID=MV,Type=Integer,Description="Mean variations in the window">
##FORMAT=<ID=IB,Type=Integer,Description="IBS number">
##FORMAT=<ID=VA,Type=Integer,Description="Variations">
##FORMAT=<ID=OB,Type=Integer,Description="Observed kmers">
##FORMAT=<ID=ID,Type=Integer,Description="Inner distance">
##FORMAT=<ID=LD,Type=Integer,Description="Left tail distance">
##FORMAT=<ID=RD,Type=Integer,Description="Right tail distance">
##FORMAT=<ID=KD,Type=Float,Description="Mean kmer depth">
##FORMAT=<ID=SC,Type=Float,Description="Score">
##PARAM=<ID=window,value=0>
##PARAM=<ID=step,value=0>
##PARAM=<ID=kmer,value=31>
##PARAM=<ID=IBS,value=false>
##PARAM=<ID=nwindow,value=72837>
##PARAM=<ID=wti,value=0.5>
##PARAM=<ID=wtt,value=0.5>
##PARAM=<ID=wtk,value=0.0>
##CMD=kcftools.jar getVariations -k lsal.chr3 -o lsal.kcftools.kcf -r lsatv11.chr3.fasta -s lsal -t 24 -w 50000

Header Line Details¶

Header Key	Description
`##format`	Version of the KCF format specification.
`##date`	Date of generation.
`##source`	Software/tool that created the file.
`##reference`	Reference genome FASTA file used in analysis.
`##contig`	Reference contig ID and its length.
`##INFO`	Window-level summary statistics (score, kmers, variations).
`##FORMAT`	Sample-level metrics (e.g., IB, VA, OB, etc.)
`##PARAM`	Runtime parameters used in the tool.
`##CMD`	Full command used to generate the KCF file (for reproducibility).

KCF File Data Columns¶

Each row of the file (after headers) represents a non-overlapping genomic window with its variation summary.

Main Columns¶

Column	Description
`CHROM`	Reference chromosome or contig name.
`START`	Start coordinate of the window (0-based).
`END`	End coordinate of the window (0-based, exclusive).
`TOTAL_KMERS`	Total reference k-mers in the window.
`INFO`	Semicolon-separated list of window-level stats (IS, XS, MS, etc.).
`FORMAT`	Format string that defines the sample field structure (e.g., IB:VA:OB:...).
`<Sample>`	Sample-specific colon-separated values based on the `FORMAT`.

Format Field Attributes¶

Sample fields are defined based on the FORMAT column and provide detailed metrics per window.

Field	Description
`IB`	Identity-by-state number (shared k-mers)
`VA`	Number of variations detected in the window
`OB`	Number of observed k-mers (sample-specific presence)
`ID`	Inner distance (gap within the window between k-mer hits)
`LD`	Left tail distance (gap at the beginning of the window)
`RD`	Right tail distance (gap at the end of the window)
`KD`	mean k-mer depth in the window
`SC`	Identity score (e.g., percentage similarity between sample and reference)

Note

All coordinates follow the 0-based BED-style convention.
The FORMAT field is essential for decoding sample data.
INFO fields are useful for filtering or plotting summaries at a per-window level.

Example Data Row¶

chr3    0       50000   1012    IS=0.91;XS=1.00;MS=0.95;IO=980;XO=1000;MO=990;IV=0;XV=3;MV=1     IB:VA:OB:ID:LD:RD:KD:SC     989:0:990:0:0:0:10.85:99.95

This row shows: - A 50kb window on chromosome 3 - 1012 k-mers total - High identity score (99.95) - 0 variations detected - Sample-specific field values are provided in the last column