Translate VCF

Takes vcf file input and determines functional consequence of mutations with regard to UCSC known genes, refseq genes or ensembl genes. Will use UCSC known gene annotation by default. A correctly formatted CDS file must be used containing CDS sequences and gene table info (i.e. info from knownGene.txt for UCSC genes, refGene.txt for RefSeq or ensGene.txt for ensembl as downloaded from the UCSC downloads page [http://hgdownload.cse.ucsc.edu/downloads.html or ftp://hgdownload.cse.ucsc.edu/]) for the relevant gene set. This CDS file can be created using extractCDS.pl script or using the --DOWNLOAD_NEW option of this script.