faToVcf requires that the reference sequence be included in the MSA input, and expects it to appear first by default -- if users don't know that, then they could end up with incorrect VCF. This change adds some example commands to show how to specify the correct reference sequence if it is not first in the MSA file, and how to add it if it is not included in the MSA file.
faToVcf requires that the reference sequence be included in the MSA input, and expects it to appear first by default -- if users don't know that, then they could end up with incorrect VCF. This change adds some example commands to show how to specify the correct reference sequence if it is not first in the MSA file, and how to add it if it is not included in the MSA file.