I am looking for a recent comparison of variant effect prediction tools.
There is this older paper from 2013/2014 that argues that choice of transcript data set and variant effect prediction tool has a large effect on variant effect annotation.
Choice of transcripts and software has a large effect on variant annotation http://genomemedicine.biomedcentral.com/articles/10.1186/gm543
I am guessing that choice of transcript data set still makes a large difference (kind of obvious) but I am hoping that choice of variant effect prediction tool makes less of a difference nowadays.
The SnpEff web page mentions that there was an effort to do some standardizatons among variant effect predictors to make them more comparable:
This new format specification has been created by the developers of the most widely used variant annotation programs (SnpEff, ANNOVAR and ENSEMBL's VEP) and attempts to:
provide a common framework for variant annotation, make pipeline development easier, facilitate benchmarking, and improve some known problems in variant annotations.
Did this really improve the concordance between different variant effect predictions software (especially SnpEff v.s. Ensembl VEP)?