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

Variant allele fraction was previously being calculated as: `var_reads / (var_reads + ref_reads)`. And is now calculated as: `var_reads / tot_reads`

Only one output file will now be created with the following columns:
```#CHROM  POS  REF  VAR  DEPTH  RAF  VAF  FILTER  FILTER_DETAILS```

The tags under `FILTER` can be back-filled as VCF filters using vcf-annotate. The column `FILTER_DETAILS` is a friendlier explanation of why a variant was filtered.