Query about snpEff

mikawinmikawin Posts: 9Member


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?

Thanks for your input!



  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 6,809Administrator, GATK Developer admin

    Hi Mika,

    These are questions that would be best answered by the authors of snpEff. Although we do use it ourselves on occasion, we aren't really qualified to comment on the finer points of how it works (thinking here of your second question, mostly). And we would certainly not contradict anything that you have seen on their own website :) Of course if someone from the community wants to jump in and comment here, that would be very welcome.

    Geraldine Van der Auwera, PhD

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