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Phased Heterozygous SNP
I have difficulties in understanding the genotypes of the phased SNPs. Here i have a SNP where only one read has a reference allele and 11 reads have an alternate allele and is called as heterozygous SNP.
chr15 8485088 . G T 4936.33 PASS BaseQRankSum=1.82;ClippingRankSum=0;ExcessHet=0;FS=2.399;InbreedingCoeff=0.721; MQ=60;MQRankSum=0;QD=32.86;ReadPosRankSum=0.267;SOR=1.167; DP=10789;AF=0.013;MLEAC=13;MLEAF=0.012;AN=1300;AC=28 GT:AD:DP:GQ:PGT:PID:PL 0/1:1,12:13:3:0|1:8485088_G_T:485,0,3
The genotype for a single sample from a multi-sample VCF is shown here. Could someone throw light on how to interpret the genotype as heterozygous as only one read has reference allele. It should have been called as homozygous SNP. Is this a bug or am i missing something also IGV does not show the reference read.(GATK Version=3.7-0-gcfedb67).