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.
usage: vk rename [--prefix=<prefix> --suffix=<suffix> --subst=<subst>] <vcf>
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
= to separate what you are substituting from and to:
vk rename --subst=OLD_SAMPLE_NAME:NEW_SAMPLE_NAME
The above command would rename the
N2 sample as
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