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HaplotypeCaller Missing variant with stand_call_conf 30

Dear GATK users,

I have a strange case to debug with HaplotypeCaller GATKv3.7 and -stand_call_conf 30 parameter. In essence, the below variant is found when -stand_call_conf 30 is not used and the variant is missing when -stand_call_conf 30 is used.

 chr12  54677628    .   G   A   6505.60 .   AC=1;AF=0.500;AN=2;BaseQRankSum=-12.044;DP=486;ExcessHet=3.0103;FS=1.754;MLEAC=1;MLEAF=0.500;MQ=53.96;MQRankSum=-3.227;QD=13.41;ReadPosRankSum=0.672;SOR=0.835  GT:AD:DP:GQ:PL  0/1:261,224:485:99:6513,0,8151

Could someone explain how -stand_call_conf 30 is missing this variant despite of high depth and QUAL?


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