I have a small query regarding the quality of Genotype that is reported in a VCF file. In the “PL” field there are 3 numbers for 3 types of genotypic likelihood, which is understandable. However, I have a mutation with all the numbers of the respective genotypic likelihoods to be very low(if I am calculating by 10^(PL/10) formula). Can anyone suggest me whether there is any cutoff number for the “PL” field(among the 3 numbers), which would confirm the respective genotype for the mutation?
Thanks in advance,