vcf2maf v1.1

• Now defaults to Ensembl's VEP for better HGVS format, and canonical transcript selection
• Now accepts VCFs that are already annotated with VEP or snpEff
• Supports user-specified directories for VEP/snpEff installation and DB cache
• Simplified code that prioritizes and selects transcripts to report in the MAF

For each variant, the protocol for selecting a single affected transcript is now as follows:

1. Sort effects first by transcript biotype priority, then by effect severity, and finally by transcript length
2. Pick the gene affected on the top of the list, and choose it's canonical transcript (VEP only)
3. If the gene has no canonical transcript tagged, choose its longest transcript instead