snpEff is dependent on Java 7, which is not loaded by default on Orchestra. Before using snpeEff be sure to load the module for Java 7:

module load dev/java/jdk1.7

When annotating our VCF using snpEff, we encountered a problem with accessing the genome database which was located within our home directory. Rather than giving the full path to snpEff we indicated the path relative to our current directory ('variants'). This was the source of the error.

In class we used:

-dataDir ../reference/snpeff hg19 

What we should use instead (user_name is your Orchestra login):

-dataDir /home/user_name/HBC-NGS/var-calling/reference/snpeff hg19 

It seems that snpEff (which is a Java program) is unable to interpret the unix-specific notation of moving up a parent directory, and requires the full path. If you remember with Trimmomatic (also a Java program) we ran into a similar problem with the ~ notation for home directory. Gotta love Java.