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