Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
Part of my GATK result is below. I don't understand why those called as 2/2 were not called as 1/1. I thought the second position in AD field is the depth for the first alternate allele (C in this case) and the third position in the AD field is the depth for the second alternate allele (G in this case). Do I misunderstand something?
1 745049 . A C,G 39258.66 PASS AC=29,240;AF=0.094,0.779;AN=308;BaseQRankSum=-3.240e-01;ClippingRankSum=0.509;DP=1690;FS=0.000;GQ_MEAN=33.06;GQ_STDDEV=22.58;InbreedingCoeff=0.8847;MLEAC=28,246;MLEAF=0.091,0.799;MQ=60.00;MQ0=0;MQRankSum=0.417;NCC=0;QD=26.96;ReadPosRankSum=0.509 GT:AD:DP:GQ:PL 1/2:0,2,2:4:57:135,57,78,84,0,78 0/0:13,0,0:13:7:0,7,317,7,317,317 2/2:0,0,16:16:48:464,513,765,48,51,0 2/2:0,17,0:17:51:495,495,495,51,51,0 1/2:0,1,8:9:18:311,281,333,42,0,18 2/2:0,6,0:6:18:170,170,170,18,18,0 2/2:0,14,0:14:42:398,398,398,42,42,0 2/2:0,12,0:12:36:327,327,327,36,36,0 2/2:0,8,0:8:24:205,205,205,24,24,0 2/2:0,17,0:17:51:480,480,480,51,51,0 2/2:0,10,0:10:30:287,287,287,30,30,0 0/0:11,0,0:11:20:0,20,348,20,348,3481/2:0,1,5:6:27:161,133,207,42,0,27 2/2:0,14,0:14:42:396,396,396,42,42,0 2/2:0,9,0:9:27:257,257,257,27,27,0 2/2:0,11,0:11:33:317,317,317,33,33,0 2/2:0,7,0:7:21:200,200,200,21,21,0 2/2:0,16,0:16:48:454,454,454,48,48,0 1/2:0,4,14:18:99:527,403,618,165,0,123 2/2:0,18,0:18:54:514,514,514,54,54,0 2/2:0,26,0:26:78:721,721,721,78,78,0 2/2:0,11,0:11:33:304,304,304,33,33,0 2/2:0,11,0:11:33:318,318,318,33,33,0