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A single pass mechanism to add multiple annotations to vcf


I was wondering if there is a nice way to apply multiple processing steps to each variant (or a group of variants) as they are read so that the variant file is not read again and again. My understanding is that even if I use Queue, each script would read the vcf again. Is that correct?

Best Answer


  • SheilaSheila Broad InstituteMember, Broadie ✭✭✭✭✭
  • juberjuber Member

    Hi Sheila,

    Thanks for the quick response.

    Looking at the VariantAnnotatorEngine method annotateContext, it seems that it is only doing INFO annotations and not genotype annotations (ie FORMAT fields). Also if one annotation depends on a genotype attribute added in a previous annotation, that doesn't seem accessible in the current annotation. I am trying to understand if Variant Annotator could be used to create a chain of annotations with possible dependencies on previous annotations.


    Juber Patel

  • juberjuber Member

    Hi Geraldine,

    on a second look, I do see that VariationAnnotationEngine annotates genotypes as well. But the sequence and dependency issue remains. Thanks for the clarification.


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