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