I have a genomics data from Bacteria (E. Coli.) and used GATK 4 for variant calling. I have noticed that for some samples and some loci, PL is 0,0. Can anyone please explain this?
eg. NC_000913 4473651 . C <non_ref> . . . GT:AD:DP:GQ:PL 0:2,0:2:0:0,0
How can we interpret that? becuase in this case, the GT in later steps will be "." as it will be driven from PL, when we combine and genotype the samples.
thanks in advance.