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Why do I see variant calls by haplotype caller with zero reads supporting the alternate allele?
The example variant call is shown below,
13 28608228 . A AATTTTCTCTTGGAAACTCCCATTTGAGATCATATTCATATTCTCTGAAATCAACGTAGAAGTACTCATTATCTGAGGAGCCGCTCAC 2040.73 . AC=1;AF=0.500;AN=2;DP=867;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=70.00;QD=2.35;SOR=0.105 GT:AD:GQ:PL:SAC 0/1:2,0:99:2078,0,836:0,2,0,0
I understand that haplotype caller uses certain filters. Technically this variant should not have been called if the reads remaining after applying filters is zero.