I have a vcf v4.2
file with structural variants, the 8 columns describing the variant are clear, but in the genotype information I got confused by values of GL
entries. In the vcf specification they mention that GL
are likelihoods of the individual genotypes, but as far as I am concerned, likelihood should be a number between 0 and 1, therefore I am suprised to see negative numbers. Then I thought that it might be log-likelihood, but then it's strange that the higher the number is the better. Here is a sample of 5 variants with various called genotypes
... GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV 0/1:-22.4949,0,-4.49485:45:PASS:20:1:11:0:1:4:0:0
... GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV 0/1:-3.1888,0,-43.9892:32:PASS:16:26:13:2:9:2:0:0
... GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV 0/1:-0.190635,0,-49.2888:4:LowQual:26:51:31:2:10:1:0:0
... GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV 0/0:0,-1.01435,-75.899:10:LowQual:18:54:26:2:14:1:0:0
... GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV 1/1:-19.198,-1.5031,0:15:PASS:70:0:58:0:0:5:0:0
The vcf
file was generated by delly genotyper. I followed their recommendations for germline SV calling. However, negative likelihoods are even in the vcf
specification, therefore it seems that it's not something delly
specific.
So, what exactly is GL
in vcf
files? And how do they relate to other entries GP
(genotype posterior probabilities, not in the file by delly) and GQ
(conditional genotype quality)?