kcftools kcf2plink¶

The kcftools kcf2plink command is used to convert a .kcf file into PLINK format files (.ped and .map). This allows users to leverage the KCF data for further genetic analyses using PLINK.

Usage¶

$ kcftools kcf2plink [-a=<scoreA>] [-b=<scoreB>] [--chrs=<chrsFile>]
                      -i=<inFile> [--maf=<minMAF>]
                      [--max-missing=<maxMissing>] -o=<outPrefix>
                      [--score_n=<scoreN>]

Description¶

The kcf2plink command processes a KCF file to generate PLINK-compatible files. It interprets the identity scores in the KCF file to classify genomic regions into reference, alternate, or missing categories based on user-defined thresholds. The output files can then be used for various genetic analyses, including association studies and population genetics.

Options¶

Option	Description	Default	Required
`-i`, `--input=<inFile>`	Input `.kcf`
file to convert	N/A	Yes
`-o`, `--output=<outPrefix>`	Prefix for output files (PED and MAP)	N/A	Yes
`-a`, `--score_a=<scoreA>`	Lower score cut-off
to call the reference allele	none	No
`-b`, `--score_b=<scoreB>`	Lower score cut-off
to call the alternate allele	none	No
`-n`, `--score_n=<scoreN>`	Upper score cut-off
to call a region as missing (between `score_b` and `score_n`)	none	No
`--maf=<minMAF>`	Minimum minor allele frequency to retain a region	none	No
`--max-missing=<maxMissing>`	Maximum proportion of missing data allowed per region	none	No
`--chrs=<chrsFile>`	File listing chromosomes to include (one per line)	all	No

Output¶

This feature generates two output files: - A PED file (<outPrefix>.ped) containing genotype information for each sample. - A MAP file (<outPrefix>.map) containing marker information. - These files are formatted according to PLINK specifications and can be directly used in PLINK for further analyses.

Example output files:

output.ped
output.map

Example¶

Convert a KCF to PLINK format with thresholds:

$ kcftools kcf2plink -i sample.kcf -o plink_output -a 95 -b 70 --maf 0.05 --max-missing 0.1

This command: - Treats windows with score ≥95 as reference - Treats windows with score ≥70 (but <95) as alternate - Filters out regions with MAF <5% or >10% missing data - Generates plink_output.ped and plink_output.map files for use in PLINK

Note

Score thresholds (--score_a, --score_b) are crucial to define genotype states.
MAF and missing data thresholds help clean noisy or non-informative regions.
Use the --chrs option to restrict to a subset of chromosomes if desired.
If allele scores are ambiguous or missing for a sample in a region, that entry will be marked -1.

Help¶

To get help on this command, run:

$ kcftools kcf2plink --help