When processing a BCF file, we can either calculate our own genotype likelihoods from the AD fields, or use the values calculated in a GL or PL field. Creating an option to dng-call and dng-loglike would allow the user to choose which data in the BCF is used.
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.
PL : the phred-scaled genotype likelihoods rounded to the closest integer (and otherwise defined precisely as the GL field)
reedacartwright
commented
7 years ago
When processing a BCF file, we can either calculate our own genotype likelihoods from the AD fields, or use the values calculated in a GL or PL field. Creating an option to dng-call and dng-loglike would allow the user to choose which data in the BCF is used.
https://samtools.github.io/hts-specs/VCFv4.2.pdf