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Adding Custom Annotation in the FORMAT field


Not sure whether this is the right place to put this, or even the right forum to ask but I was wondering whether it was possible to add custom annotations to the FORMAT field rather than the INFO field? If not GATK, do any third party programs able to handle such a request?

Thanks! Appreciate any help.


  • pdexheimerpdexheimer Member ✭✭✭✭

    It's hard to say, because it's not clear to me exactly what you're after. The VCF spec allows annotations in either the INFO or FORMAT fields, I don't think either field has different restrictions than the other (i.e., if it's valid in INFO, it's valid in FORMAT). I don't believe there are any GATK tools that will allow you create a new annotation and fill in values for that annotation in an existing VCF file (whether it's an INFO or a FORMAT annotation). However, you could certainly accomplish that by writing your own GenotypeAnnotation and giving it to VariantAnnotator. Alternatively, there may be an existing annotation that does what you want

  • ADingoAteMyBabyADingoAteMyBaby NYCMember
    edited December 2014

    Thanks for the answer. Yeah - rather than a general custom annotation (INFO) - I'm after a sample-level annotation (to be put where GT:PL:GL information is). VCF-tools certainly lets you annotate your vcf with your own custom annotations - however, only as a general annotation (ie in the INFO fields). I had a hard time finding a tool that allows for custom annotation to put at sample-level but I think GenotypeAnnotation might have to be the way to go if it allows me to add sample-level annotation.

  • pdexheimerpdexheimer Member ✭✭✭✭

    Personally, I would probably do it in Perl

  • sibsccsibscc sibsMember
  • tommycarstensentommycarstensen United KingdomMember ✭✭✭

    @ADingoAteMyBaby‌ bcftools can do that:
  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    @pdexheimer said:
    Personally, I would probably do it in Perl

    Man, that's pretty old-school ;)

    (now, if you had said Python...)

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    @ADingoAteMyBaby Ultimately what it really depends on is what you're using as annotation source. Are you trying to annotate sequence context info, or metadata about the samples, or something else? And what format is the information in? VariantAnnotator can transfer annotations from one VCF to another, for example, which can be pretty useful. Otherwise, there's another software package from the Broad called Oncotator that is a really powerful annotation engine (and despite the name, is not cancer-specific). We host its docs on our forum here:

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