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How does GATK determine GT when calling variants?
Looking closely at our vcf file produced by HaplotypeCaller we noticed disagreement between PL values and GT in some variants.
1 762589 rs71507461 G C 21714.69 PASS [clipped] GT:AD:DP:GQ:PL 1/1:0,33:33:99:1464,99,0 **0/1**:32,38:70:99:**0,9,2274** **0/1**:78,42:120:99:**323,30,0** **1/1**:11,5:96:99:**123,0,324** 1/1:2,84:86:99:3923,271,0 1/1:2,104:106:99:4945,348,0 1 762592 rs71507462 C G 21714.69 PASS [clipped] GT:AD:DP:GQ:PL 1/1:0,60:32:99:1464,99,0 0/1:586,0:67:99:1471,0,2274 0/1:77,42:119:99:1667,0,6152 1/1:1,95:96:99:4462,310,0 1/1:2,85:87:99:3923,271,0 1/1:2,101:103:99:4945,348,0 1 762601 rs71507463 T C 21714.69 PASS [clipped] GT:AD:DP:GQ:PL 1/1:1675,144:32:99:1464,99,0 0/1:30,38:68:99:1471,0,2274 0/1:79,42:121:99:1667,0,495 1/1:20,24:90:99:4462,0,476 1/1:2,83:85:99:3923,271,0 1/1:3,107:110:99:4945,348,0
What is the relationship between GT and PL - I initially thought PL determined GT? What other factors go into GATK deciding on a particular GT? For example, does GATK take into account the GT of nearby variants to determine the GT of an individual variant?
Thank you in advance for your help.