Why does IGV turn a VCF QUAL of "." into -10?
Looks like they are treating the "." as a value of 1.  According to the VCF spec the quality is "−10log10 prob".  Where are you getting your QUALs from?  I have never seen the quals as a "." and IGV probably needs to do some translation into an int but a QUAL of -10 makes no sense. 

I would report it and let them explain.