calculating genotype probabilities (GP) from phred-scaled genotype likelihood

Question

[markova]

I used samtools mpileup to generate PL values (the phred-scaled genotype likelihoods). I need to generate vcf/or Beagle file with genotype probabilities (GP). I have found that the script vcf2gen_v1.1.pl will calculate genotype probs from GL or PL, but I cannot find it. Is there some script available that will do the same job? Thanks.

[barslmn]

I don't think you can calculate GP from GL.

https://samtools.github.io/hts-specs/VCFv4.3.pdf

GP is defined as:

GP (Float): Genotype posterior probabilities in the range 0 to 1 using the same ordering as the GL field; one use can be to store imputed genotype probabilities.

GL is defined as:

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; without GT field, diploidy is assumed.

GP is imputed genotype probability and GL is about how sure you are calling genotypes. You can get the GP when you're doing the imputation with Beagle.