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?