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Variant reported by GATK is not seen in IGV
I am facing an issue with GATK 3.8. After running GATK HaplotypeCaller I get one variant detected as
Pf3D7_05_v3 133207 . A G 60 . AC=1;AF=1.00;AN=1;DP=2;FS=0.000;MLEAC=1;MLEAF=1.00;MQ=60.00;QD=30.00;SOR=0.693 GT:AD:DP:GQ:PL 1:0,2:2:90:90,0
but when i see it in IGV it does not show any such variant detected there and show the reference allele. Can anyone please help me why it is so?