From the published work I've seen, there's a common theme of looking at Tier 1 variants in sequence data, specifically: non-synonymous/non-sense mutations, splice site variants, and frameshift indels. In some cases, this is easier said then done, requiring in-phase alignment and gene annotation. Does anyone know of a tool that or collection of tools that can pull out these features simply by knowing the physical position of a variant? I know trait-o-matic is heading in this direction but I don't believe they've tackled splice sites yet.
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