Merge pull request #2 from mlinderm/adam-vcf

Adam vcf
Merge pull request #3 from mlinderm/adam-vcf

Sent varIsFiltered appropriately if FILTER is PASS or "."
Output ADAMGenotypes, and not ADAMVariant
Merge branch 'adam-vcf' of https://github.com/nealsid/adam into adam-vcf
Bare minimum ADAMGenotype to GATK VariantContext conversion