Annotates genotypes in the First dataset with genotypes from the Second adding the genotype as another flag to each sample filled in the first file. Annotation-tag is the name of the sample flag which is added to store the annotation. Also adds a 'has_variant' flag for sites where the second file has a variant.

Vcfannotate is a part of VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib).