kcftools getVariations

The getVariations command screens for reference k-mers that are not present in the KMC database, identifying candidate variations.

Usage

$ kcftools getVariations [OPTIONS]

Required Options

Option Description
-r, --reference=<refFasta> Reference FASTA file
-k, --kmc=<kmcDBprefix> KMC database prefix (omit .kmc_pre and .kmc_suf)
-o, --output=<outFile> Output file name (in KCF format)
-s, --sample=<sampleName> Sample name to associate with the output
-f, --feature=<featureType> Feature type for variation detection: window, gene, or transcript

Optional Parameters

Option Description Default
-t, --threads=<nThreads> Number of threads to use 2
-m, --memory Load entire KMC DB into memory for faster access false
--wi=<innerDistanceWeight> Weight for inner k-mer distance in scoring 0.3
--wt=<tailDistanceWeight> Weight for tail k-mer distance in scoring 0.3
--wr=<kmerRatioWeight> Weight for k-mer ratio in scoring 0.4
-w, --window=<windowSize> Window size in base pairs (used with --feature=window) N/A
-g, --gtf=<gtfFile> GTF file with annotations (required for gene or transcript features) N/A
-c, --min-k-count=<minKmerCount> Minimum k-mer count threshold to consider valid 1
-p, --step=<stepSize> Step size in base pairs for sliding windows (used with --feature=window) windowSize

Examples

Detect variation in 1000 bp windows:

$ kcftools getVariations -r ref.fa -k sample_kmc -o sample.kcf -s sample_name -f window -w 1000

Detect variation in genes using GTF:

$ kcftools getVariations -r ref.fa -k sample_kmc -o sample.kcf -s sample_name -f gene -g annotations.gtf

Custom k-mer weights and multithreading:

$ kcftools getVariations -r ref.fa -k sample_kmc -o sample.kcf -s sample_name -f window -w 1000 --wr 0.5 --wi 0.2 --wt 0.3 -t 8 -m

Note

  • Ensure your KMC database was generated with compatible parameters (e.g., k-mer size) relative to the reference genome.
  • Use appropriate --feature settings depending on your annotation and biological context.
  • The output .kcf file can be used for downstream analysis with other kcftools commands like findIBS or kcfToMatrix.

Help

To display command-line help:

$ kcftools getVariations --help