Are you looking for something like the Ensembl Variation Effect Predictor?

This is a Perl script that can do what you want (or if not exactly can be adjusted quite easily yourself to add other types of consequences.

Also, did you check snpEff?

You should take a look at other SNP annotation related questions:

SNP location annotation

variant effect predictor / annotator

In my experience, Annovar is very easy to use, well documented, supports various SNP file formats and provides flexibility in regards to the different types of supported annotations. (basically, any table you can download from UCSC can be used to annotate a SNP list)

good luck

Check out snpEff, it's a java jar that will run anywhere you have java. My favorite variant annotator. And it's super fast! snpEff!

Hey,

thanks for the fast response. I am a bit experienced with snpEff, but I did not know, that it can handle INDELs. Thats cool. Also the Ensembl Variation Effect Predictor looks interesting.

Thank you all!

You could check out OpenCRAVAT, it will annotate variants including indels. Unlike tools like annovar, you can run it simply from either the command line or through a graphical user interface.