NON_REF in gvcf
I see something like this
chr1 17697 . G C, 72.77 . BaseQRankSum=0.322;ClippingRankSum=-1.517;DP=8;MLEAC=1,0;MLEAF=0
.500,0.00;MQ=40.00;MQ0=0;MQRankSum=0.322;ReadPosRankSum=0.956 GT:AD:DP:GQ:PL:SB 0/1:5,3,0:8:99:101,0,178,116,187,303:0,5,0,3
in my gvcf file.
apparently NON_REF was treated as an allele and was assigned a read depth (0 in this case) and genotype likelihood in combination with G, C alleles
It is very confusing!