My karyotype is 46,XY,22qs+/45,X,22qs+. The 22qs+ is an exceedingly rare but familial improperly-satellited autosome. The rest is just mosaicism. Some of my cells are XY (ordinarily male) and others are XO (ordinarily female with Turner Syndrome).
In my VCF file, however, most of my X chromosome variants are GT: 1/1. All of my Y chromosome variants are GT: 1/1, except the intergenic ones, which are all GT: 0/1. The lab insists that the allele counts are legit.
So how do I reconcile that with my karyotype? Or am I misunderstanding the VCF information?
Here's one of the variant records:
chrX 2700157 . G A 1219.77 PASS AC=2;AF=1.00;AN=2;DP=34;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=34.24;SOR=2.049;set=variant2 GT:AD:DP:GQ:PGT:PID:PL:CGIANN_VARNAME:CGIANN_1000GAF:CGIANN_ESP6500AF 1/1:0,34:34:99:1|1:2700150_G_C:1248,102,0:NM_175569.2(XG) c.178G>A (p.Asp60Asn),NM_175569.2(XG) c.178G>A (p.Asp60Asn):0.07,0.07:0.101969,0.101969