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Question: VCF annotation, logic, Annovar, VEP, snpEff
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gravatar for vaish01kv
20 months ago by
vaish01kv • 0
India
vaish01kv • 0 wrote:

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 • 529 views
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modified 20 months ago by Pierre Lindenbaum ♦ 133k • written 20 months ago by vaish01kv • 0
1
gravatar for Pierre Lindenbaum
20 months ago by
Pierre Lindenbaum ♦ 133k
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum ♦ 133k wrote:
  • 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
ADD COMMENT • link written 20 months ago by Pierre Lindenbaum ♦ 133k

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.

ADD REPLY • link written 20 months ago by vaish01kv • 0

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

ADD REPLY • link modified 20 months ago • written 20 months ago by vaish01kv • 0
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