Calculate and add VAF during variant normalisation

[imedina]

A very useful variant filter, especially in cancer analysis, is the Variant Allele Fraction (VAF). Unfortunately, this is not typically provided by variant callers, but we can easily calculate it during variant normalization. For this first implementation, several somatic callers and default germline callers are supported.

This creates a new VCF format field called EXT_VAF that will be indexed in OpenCGA allowing indexed filtering.