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GT, PL and GQ inconsistent
From the GATK documentation I found that for PL field, the most likely genotype (assigned in the GT field) is 0. However, from the vcf file called by GATK, I found that this is not always the case. Below are a few examples:
Also, GQ is equal to the second smallest PL, unless that PL is greater than 99. However, I also found cases like the following, where the GQ is 1.76:
I am wondering that whether they have specific meanings or it is due to calling error, or due to the low quality of calling. Thank you very much.