VT and Recall issue with multivariants in same position.

[elleira]

Description of the bug

If a caller finds larger variant and a smaller (one) base substitution in the same region, vt will split the larger variant up into two variants. The caller then has two separate but identical calls in the same position with very different AF, recall then only includes the first of these two variants which then can severely skew the result.

Ref	G	C	AF
Alts	A	G	3 %
		G	22 %
After normalization	A		3 %
		G	3 %
		G	22 %
After recall	A		3 %
		G	3 % (should be 25 %?)

One solution could be to combine the two calls in the same position and add the AF to make sure all information is included.