Output genotypes as vcf

This will output genotypes as vcf if the output path ends in VCF, originally I had a flag, but the current vcf writer won't without a vcf extension.

This is somewhat odd output, in that the folder has a vcf extension, but the part file contained does not, it would part-r-0000.  There is a coalesce to only create a single part file (not multiple files each with a header