IGV is turning QUAL "." into -10 from this VCF of structural variations. I'm wondering if this means anything or if I should report a bug to the IGV devs.
Here's a row from a VCF:
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMPLE chrY 11292098 DUP00008569 C <DUP> . PASS IMPRECISE;SVTYPE=DUP;SVMETHOD=EMBL.DELLYv0.8.1;CHR2=chrY;END=56834684;PE=3;MAPQ=24;CT=5to3;CIPOS=-265,265;CIEND=-265,265 GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV0/1:-5.71458,0,-20.0913:57:PASS:0:90774:0:-1:6:5:0:0
You see the QUAL value is "."
IGV reports it as -10
(This call is probably a false positive but it's just an example. There are others)