The Frontline Support team will be offline December 17-18 due to an institute-wide retreat and offline December 22- January 1, while the institute is closed. Thank you for your patience during these next few weeks as we get to all of your questions. Happy Holidays!
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.