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Test-drive the GATK tools and Best Practices pipelines on Terra
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Reading haplotype caller
6 31324601 rs9281379 C CA,CG 158601.1 . AC=1,1;AF=0.500,0.500;AN=2;DB;DP=3697;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=59.26;QD=29.97;SOR=0.751 GT:AD:DP:GQ:PL 1/2:0,1756,1926:3682:99:158618,52177,41139,71967,0,65397
With respect to the output of haplotype caller, can you please explain what does "1/2" mean in genotype?
Is it that the reference allele is not present in the sequence and one strand has CA and other has CG?