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Sheila
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Broad Institute
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  • ga23981
    Hi Sheila,
    I see a lot of GT calls as 0:4, 0:5 so on and so forth in my gvcf file. I used HaplotypeCaller on the bacterial samples with ploidy 1. Are such calls expected? Could you suggest me what needs to be done with such calls?

    NZ_CP020943.1 6169 . G A 51.79 PASS AC=1;AF=0.029;AN=34;DP=46;FS=0.000;MLEAC=1;MLEAF=0.029;MQ=40.00;QD=25.89;SOR=2.303 GT:AD:DP:GQ:PL .:0,0 0:1,0:1:41:0,41 .:0,0 0:2,0:2:82:0,82 .:0,0 .:0,0 .:0,0 0:1,0:1:41:0,41 .:0,0 .:0,0
    NZ_CP020943.1 6175 . C T 51.66 PASS AC=1;AF=0.029;AN=35;DP=48;FS=0.000;MLEAC=1;MLEAF=0.029;MQ=40.00;QD=25.83;SOR=2.303 GT:AD:DP:GQ:PL .:0,0 0:1,0:1:41:0,41 .:0,0 0:2,0:2:82:0,82 .:0,0 .:0,0 .:0,0 0:1,0:1:41:0,41 .:0,0 .:0,0
    NZ_CP020943.1 6323 . T C 286.33 PASS AC=2;AF=0.026;AN=78;DP=303;FS=0.000;MLEAC=2;MLEAF=0.026;MQ=40.00;QD=31.81;SOR=4.615 GT:AD:DP:GQ:PL 0:4,0:4:99:0,126 0:3,0:3:99:0,114 0:3,0:3:99:0,100 0:3,0:3:99:0,113 0:1,0:
    NZ_CP020943.1 6346 . A G,C 1163.86 PASS AC=3,2;AF=0.038,0.026;AN=78;DP=332;FS=0.000;MLEAC=3,2;MLEAF=0.038,0.026;MQ=40.00;QD=26.28;SOR=6.736 GT:AD:DP:GQ:PL 0:4,0,0:4:99:0,126,126 0:3,0,0:3:99:0,114,114 0:3,0,0:3:99:0,122,122 0:3,0,0:3:96:0
    NZ_CP020943.1 6352 . G C 693.29 PASS AC=3;AF=0.038;AN=78;DP=335;FS=0.000;MLEAC=3;MLEAF=0.038;MQ=40.00;QD=29.45;SOR=5.670 GT:AD:DP:GQ:PL 0:4,0:4:99:0,126 0:3,0:3:99:0,114 0:3,0:3:99:0,122 0:3,0:3:99:0,113 0:2,0:
    NZ_CP020943.1 6388 . G A 371.13 PASS AC=1;AF=0.013;AN=79;DP=377;FS=0.000;MLEAC=1;MLEAF=0.013;MQ=40.00;QD=33.74;SOR=4.977 GT:AD:DP:GQ:PL 0:4,0:4:99:0,126 0:3,0:3:99:0,114 0:3,0:3:99:0,122 0:5,0:5:99:0,170 0:3,0:
    NZ_CP020943.1 6418 . T C 425.13 PASS AC=1;AF=0.013;AN=79;DP=450;FS=0.000;MLEAC=1;MLEAF=0.013;MQ=40.00;QD=30.35;SOR=5.136 GT:AD:DP:GQ:PL 0:4,0:4:99:0,126 0:3,0:3:99:0,114 0:3,0:3:99:0,122 0:5,0:5:99:0,170 0:3,0:
    NZ_CP020943.1 6437 . T C 1172.13 PASS AC=1;AF=0.013;AN=79;DP=460;FS=0.000;MLEAC=1;MLEAF=0.013;MQ=40.00;QD=30.97;SOR=6.932 GT:AD:DP:GQ:PL 0:4,0:4:99:0,126 0:3,0:3:99:0,114 0:3,0:3:99:0,122 0:5,0:5:99:0,170 0:3,0:
    NZ_CP020943.1 6718 . C G 916.10 PASS AC=2;AF=0.025;AN=80;DP=1168;FS=0.000;MLEAC=2;MLEAF=0.025;MQ=40.00;QD=28.92;SOR=6.593 GT:AD:DP:GQ:PL 0:25,0:25:99:0,945 0:3,0:3:99:0,114 0:3,0:3:99:0,122 0:5,0:5:99:0,170 0:3,0:
    NZ_CP020943.1 6760 . T C 3718.10 PASS AC=2;AF=0.025;AN=80;DP=1985;FS=0.000;MLEAC=2;MLEAF=0.025;MQ=41.36;QD=30.99;SOR=2.115 GT:AD:DP:GQ:PL 0:25,0:25:99:0,945 0:3,0:3:99:0,114 0:49,0:49:99:0,1800 0:5,0:5:99:0,170 0:3,0:
    January 29