How does GATK determine GT when calling variants?

rosalierosalie Posts: 3Member
edited September 2013 in Ask the GATK team

Looking closely at our vcf file produced by HaplotypeCaller we noticed disagreement between PL values and GT in some variants. For example.

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.


Post edited by Geraldine_VdAuwera on


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