Remove Genome::File::Vcf object

We'll use Genome::File::Vcf::Reader/Writer) instead
Use Vcf::Reader instead of parsing vcf file by hand
Removed unused gmt

was last run 2012.3.2 and isn't used by anything in Genome
gmt annotate adaptor vcf uses Genome::File::Vcf::Reader
sub in DV2 Filter FalsePositive uses Genome::File::Vcf::Reader
add Genome::File::BedPe::Writer