VCF Liftover header stringency
I am trying to liftover from NIST b37 to hg19. I have all the files I need and I can kick off the liftover just fine, but I keep running into problems because the NIST vcf has tags in the variant line INFO field that are not in the header.
##### ERROR MESSAGE: Key PLHSWG found in VariantContext field INFO at chr1:52238 but this key isn't defined in the VCFHeader. We require all VCFs to have complete VCF headers by default
I identified about 90 tags that are not properly documented in the header.
Is there a way to ignore all of these INFO header lapses?