Tools annotation variations within gene

Question

[zhaouu]

I want to annotation variations(SNPs,INDELs) in genome, I have used snpeff to check some variations in genome, but suppose a insertion in exon and a deletion in other position in this exon. When annotate this two variation separately, they all changed gene function. but when consider them at the same time, the gene function not changed. I think common annotation tools like snpeff will not worked in this situation. So I want to know is there have any tools to solve this problem?

Answer 1

[Ashutosh Pandey]

Most of the annotators approach variants locally i.e. considering the effect of that single variant on the gene. I don't think any tool takes into account all proximal and distal mutations that can nullify the effect of a given mutation. A particular case that I always come across is two adjacent or consecutive SNPs where presence of first SNP introduces premature stop codon but this effect is nullified by the adjacent SNP. But the annotator still annotated that SNP as nonsense. I have reported this to different annotator tools but I think implementing this change (looking for variant affect globally) may drastically increase the running time.