Hi,
I have the below variant from GATK Haplotype caller and annotated as 1/1 which means homozygous for the alternate allele.
chr1 10023229 . G A 101.03 . AC=2;AF=1.00;AN=2;BaseQRankSum=-0.742;DP=49;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=8.21;MQ0=42;MQRankSum=0.742;QD=2.06;ReadPosRankSum=-0.742 GT:AD:DP:GQ:PL 1/1:42,7:47:12:129,12,0
However, the AD column shows there are 42 reads for reference and 7 reads for alternate allele. Could someone comment on this snp being reported as homozygous for alternate allele despite of having very few reads supporting it.