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VCF annotation, logic, Annovar, VEP, snpEff

I'm trying to annotate vcf file obtained manualy. Can someone please help me with the algorithm that is behind most of the annotation tool like annovar, SnpEff, VEP & other annotation tools?

variant annotation algorithm
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updated by Pierre Lindenbaum Pierre Lindenbaum • written by vaish01kv • vaish01kv

1 answer

  • get the transcript overlapping a variant
  • get the reference sequence overlapping this transcript.
  • go from 5' transcript to 3' transcript: build a virtual cDNA wild and mutated.
  • translate both cDNAs
  • compare the proteins, find if there is a difference at the position of the variant
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written by Pierre Lindenbaum Pierre Lindenbaum

Thank you so much. This is so crisp & clear. It would be even more helpful if you can help me with questions like i) where exactly databases like 1000g plays a role? ii) calculating pathogenicity score & iii) inferring allele frequency from info field.

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written by vaish01kv • vaish01kv

Could you please elaborate? Also it would be really helpful if you get me any journal explaining this.

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written by vaish01kv • vaish01kv

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