How is AC calculated?

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mk

• April 12, 2020 22:30

I am having trouble understanding how AC is calculated. Please see the following 2 lines in a VCF:

X 2234 . A G 110933.03 PASS AC=2;AF=1.00;AN=2;DP=2914;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=34.50;SOR=1.267 GT:AD:DP:GQ:PL 1/1:0,2914:2914:99:110947,8753,0

X 24345 . G A 3084.60 QD_filter AC=1;AF=0.500;AN=2;BaseQRankSum=-1.356;DP=6964;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.99;MQRankSum=-3.317;QD=0.44;ReadPosRankSum=-2.227;SOR=0.724 GT:AD:DP:GQ:PL 0/1:6373,583:6956:99:3092,0,245758

Why is AC 2 in the first line, and 1 in the second line?

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  Bhanu Gandham

  • April 19, 2020 05:33

  Hi ,

  The GATK support team is focused on resolving questions about GATK tool-specific errors and abnormal results from the tools. For all other questions, such as this one, we are building a backlog to work through when we have the capacity.

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