Quality GL entries in vcf file
The VCF spec clearly states that these are indeed log likelihood values:


  • GL : genotype likelihoods comprised of comma separated floating point log10-scaled likelihoods for all possible
  genotypes given the set of alleles defined in the REF and ALT fields. In presence of the GT field the same
  ploidy is expected and the canonical order is used; without GT field, diploidy is assumed. If A is the allele in
  REF and B,C,... are the alleles as ordered in ALT, the ordering of genotypes for the likelihoods is given by:
  F(j/k) = (k*(k+1)/2)+j. In other words, for biallelic sites the ordering is: AA,AB,BB; for triallelic sites the
  ordering is: AA,AB,BB,AC,BC,CC, etc. For example: GT:GL 0/1:-323.03,-99.29,-802.53 (Floats)


With log-likelihood values, the higher the number, the better the value. So -2 is better than -3.