GenotypeGVCFs shows <NON-REF> flag despite all reads in all samples supporting the reference allele
I have been jointly genotyping variants in my samples using GenotypeGVCFs but a few sites show a flag despite all reads in all samples supporting the reference allele. Do you know why this might be the case?
chr2 37521 . T 66.18 PASS AC=0;AF=0.00;AN=30;DP=320;InbreedingCoeff=-0.0000;MLEAC=0;MLEAF=0.00;MQ=64.28 GT:AD:DP:RGQ 0/0:22,0:22:63 0/0:27,0:27:66 0/0:17,0:17:48 0/0:17,0:17:42 0/0:31,0:31:63 0/0:25,0:25:60 0/0:15,0:15:36 0/0:22,0:22:63 0/0:26,0:26:72 0/0:22,0:22:60 0/0:28,0:28:81 0/0:22,0:22:60 0/0:20,0:20:57 0/0:12,0:12:33 0/0:14,0:14:42
Thank you in advance for your help.