kcftools findIBS

The findIBS command in kcftools is used to identify Identical-By-State (IBS) or Variable Regions in a KCF (K-mer Comparison Format) file. The type of region detected depends on whether the --var flag is used.

Usage

$ kcftools findIBS [--bed] [--summary] [--var] -i=<inFile> 
             [--min=<minConsecutive>] -o=<outFile> 
             [--score=<scoreCutOff>]

Options

Option Description Default
-i, --input=<inFile> Input KCF file name (required) N/A
-o, --output=<outFile> Output KCF file name (required) N/A
--min=<minConsecutive> Minimum number of consecutive windows required for detection 4
--score=<scoreCutOff> Score cut-off percentage for defining IBS/variable windows 95.00
--bed Write output in BED file format false
--summary Write summary TSV file false
--var Detect Variable Regions instead of IBS regions false

Description

By default, kcftools findIBS detects IBS windows, which are stretches of the genome where samples are highly similar (based on the score threshold). When the --var flag is used, it instead detects Variable Regions, where the similarity score falls below the threshold—indicating higher variation.

IBS vs Variable Regions

Mode Meaning
IBS Detects windows with similarity above the threshold, indicating shared genetic regions
Variable Detects windows with similarity below the threshold, indicating higher divergence

Example

$ kcftools findIBS --input=input.kcf --output=ibs_regions.kcf --score=98.0 --min=5

This command finds IBS regions where the similarity score is ≥98.0 and stretches are at least 5 consecutive windows long.

$ kcftools findIBS --input=input.kcf --output=variable_regions.kcf --var --score=90.0

This command finds variable regions (regions with similarity <90.0).

Output

Depending on the options used, kcftools findIBS may produce:

  • A filtered .kcf file (--output)
  • A BED format file (--bed)
  • A summary .tsv file (--summary)