kcftools cohort¶

The cohort command allows you to combine multiple KCF files (each representing an individual sample) into a single cohort file. This is essential for performing joint analyses across multiple samples, such as identifying shared or unique variation patterns.

Usage¶

$ kcftools cohort [OPTIONS]

Required Option¶

• -o, --output=<outFile>
  Output file name for the resulting cohort KCF file.

Input Options (one of the following is required)¶

You must specify either --input or --list to provide sample KCF files.

• -i, --input=<inFiles>[,<inFiles>...]
  A comma-separated list of individual sample .kcf files.
  Example: sample1.kcf,sample2.kcf,sample3.kcf

• -l, --list=<listFile>
  A plain text file with one .kcf file path per line.

Example Usages¶

Combine samples using --input¶

$ kcftools cohort \
--input sample1.kcf,sample2.kcf,sample3.kcf \
--output cohort.kcf

This command will merge the three sample .kcf files into one file named cohort.kcf.

Combine samples using a list file¶

Suppose you have a file sample_list.txt with the following contents:

sample1.kcf
sample2.kcf
sample3.kcf

Run the following:

$ kcftools cohort \
--list sample_list.txt \
--output cohort.kcf

This is especially useful when working with large cohorts of samples.