Bug? Positions with reference values are listed as "Novel Variants"

[Sylvester]

I have noticed this bug in bigY results of kits that were done in August.
Positions with reference or "?" values are listed as "Novel Variants".
Is it correct? I think it is not.

Please, check these positions:

Position Ref Gen Conf //snp
----------------------------------------------
4902514 A ? Unknown L784 (A->T)
7883549 G G High L800 (G->A)
8684839 T T High L802 (T->C)
9879005 C C High L858 (C->T)
14028228 T T High L804 (T->A)
14236879 A A High L791 (A->C)
14263127 G G High L862 (G->T)
15134176 G G High L808 (G->A)
15668177 C C High L795 (C->T)
16018726 C C High P321 (C->T)
16699291 A A High L805 (A->G)
17599534 T T High L803 (T->C)
18146894 C C High L782 (C->G)
18162467 G G High L793 (G->T)
18180367 T T High L785 (T->C)
21610585 C C High L968 (C->T)
21779257 A A High --
21898355 T T High --
21900946 T T High L807 (T->G)
22725125 C C High L790 (C->T)

[wkauffman]

Look at the VCF file at that position to see if this is an INDEL (insertion or deletion).

[Sylvester]

I have just noticed that two of them were recently added to my novel-list(my bigY was done a year ago).
And it looks like no INDELs in vcf:

chrY 9879005 . C . 1484.13 PASS . GT 0
chrY 14263127 . G . 103.184 PASS . GT 0