I am planning to use snpEff to map my variant data (SNPs & Indels) to genes data.
My query is
Can snpEff handle vcfs with both Indels as well as SNPs? (the snpEff site does indicate that it is possible, just want to confirm the same.)
Secondly, all the mappings that are done, are they done per SNP basis or per codon basis? For instance if you have two SNPs next to each other, their combined effects may change the codon (and possibly the amino acid it is coding for). Does the tool do this?