FORMAT 'PL' is not defined in the header, assuming Type=String (bcftools)

Question

[goatsrunfaster]

I am trying to use bcftools to fix references on some older VCF files I have, but I keep getting errors related to the phred-scaled genotype likelihoods (PL). see below:

(reddog) -bash-4.2$ bcftools +fixref all.mergedSNPsApril.vcf.gz -- -f Myotis_lucifugus.Myoluc2.0.75.dna.toplevel.fa -m flip > april_fixed.vcf
[W::vcf_parse_format] FORMAT 'PL' is not defined in the header, assuming Type=String
[E::main_plugin] Unchecked error (2), exiting

I received these VCFs from a collaborator and my understanding is that the alleles were pre-filtered at a certain phred, so the PL header does not exist. Any way to make bcftools just ignore it? Any help is appreciated!

[Brice Sarver]

Have you tried defining PL in the header with your favorite plain text editor or using bcftools reheader?