Hi I am trying to annotate the variants in a vcf file using snpEFF, but its giving multiple annotations for a single position. Any suggestions on how to choose the best or most appropriate one?

Thanks in advance
Firstly, I'd suggest checking some of the results with another annotation tool. Perhaps get a few of those variants giving multiple annotations and confirm the pattern with the rather popular and powerful [Variant Effect Predictor][1], or VEP. As suggested already in the comments here, the multiple annotation will be due to alternatively splicing and there is nothing much we can do apart from trying to chose one or a few "best" ones based on certain parameters and based on the question you want to answer, really. Let's suppose you are interested in the most severe consequence of a given variant. If so, choose the most severe consequence with the VEP(--[most_severe][7] flag). If you want to focus on the reliability of a transcript, you can pick the annotations for [Ensembl genes][2] that are golden (identical annotation between Ensembl and HAVANA). You can also filter out those that have lower [TSL][3] (use the [--tsl][4] flag on the VEP script) or choose the 'canonical' (find out what is deemed as [canonical transcript][5] by Ensembl) transcript (use the [--canonical][6] flag), and so on so forth...

  [1]: http://www.ensembl.org/info/docs/tools/vep/index.html
  [2]: http://www.ensembl.org/Help/Glossary?id=78
  [3]: http://www.ensembl.org/Help/Glossary?id=492
  [4]: http://www.ensembl.org/info/docs/tools/vep/script/vep_options.html#opt_tsl
  [5]: http://uswest.ensembl.org/Help/Glossary?id=346
  [6]: http://www.ensembl.org/info/docs/tools/vep/script/vep_options.html#opt_canonical
  [7]: http://www.ensembl.org/info/docs/tools/vep/script/vep_options.html#opt_most_severe