Question: VCF annotation, logic, Annovar, VEP, snpEff
gravatar for vaish01kv
20 months ago by
vaish01kv0 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?

ADD COMMENTlink modified 20 months ago by Pierre Lindenbaum133k • written 20 months ago by vaish01kv0
gravatar for Pierre Lindenbaum
20 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum133k 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 COMMENTlink written 20 months ago by Pierre Lindenbaum133k

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 REPLYlink written 20 months ago by vaish01kv0

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

ADD REPLYlink modified 20 months ago • written 20 months ago by vaish01kv0
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