Correct HGVS nucleotide names to be indexed from the start of the reference genome

[miseminger]

Currently, the HGVS nucleotide names from the VCFs, created by SnpEff, give the nucleotide mutation position as referenced from the start of the protein. HGVS recommendations require the position to be given with respect to the reference nucleotide sequence.

So, we can either:

1. rewrite those positions to match the number in the pos column, or
2. put the transcript identifier in brackets, eg. NG_012232.1(NM_004006.2):c.93G>T