The rename command can be used to add a prefix or suffix to sample names, or to substitute a sample names. Note that the command outputs an entirely new VCF to stdout. Therefore, it is best to use it within a pipe prior to output.

  vk rename [--prefix=<prefix> --suffix=<suffix> --subst=<subst>] <vcf>


  • --prefix
  • --suffix
  • --subst


When comparing VCFs, you may want to make clear the source of the samples - hence the need to add a prefix or suffix. vk rename can be used to add a prefix to all sample names using:

vk rename --prefix="GATK_" <vcf/stdin>

A suffix can be added to all sample names similarly:

vk rename --suffix="_BCFTOOLS" <vcf/stdin>

You can substitute the name of a single sample using --subst. Use a :, ,, or = to separate what you are substituting from and to:


The above command would rename the N2 sample as REFERENCE_SAMPLE.

Multiple sample names can be substituted. as well.

vk rename --subst=N2:REFERENCE_SAMPLE --subst WN2001=ANOTHER_RENAME

Rename commands can be combined as well. Substitutions are performed first, followed by adding a prefix, and finally adding suffixes.

vk rename --prefix PREFIX_ --suffix _SUFFIX --subst=N2:REFERENCE_SAMPLE