Fixed allele-fraction, improved docs, support for generic VCFs

Note that only one output file will be created with the following columns:
#CHROM  POS  REF  VAR  DEPTH  RAF  VAF  FILTER  FILTER_DETAILS

The tags within the FILTER column can be back-filled into a VCF using vcf-annotate. The column FILTER_DETAILS is a friendlier explanation of why a variant was filtered.