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VCF Liftover header stringency

hintzenhintzen Posts: 4Member

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?

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Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 6,073Administrator, GATK Developer admin

    You can probably work around this using --unsafe LENIENT_VCF_PROCESSING but keep in mind there's a good reason why this argument is called unsafe... And if you experience issues down the road with this VCF, we won't be able to provide any support (using an unsafe argument is a bit like voiding the warranty on an electronic device).

    It would be much better to just fix your headers so they are valid.

    Geraldine Van der Auwera, PhD

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