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Phred-scaled genotype likelihoods (PL)

Definition
AI-generated

In VCF, PL is a comma-separated list of Phred-scaled genotype likelihoods for the possible genotypes consistent with the called alleles and the assumed Ploidy at the site.

Topics
Sequencing Data Analysis Formats
Related
Genotype Genotype likelihood Genotype quality (GQ)

Why it matters in GWAS

PL underpins Genotype quality (GQ) and many filters on sequencing call sets; tools that regenotype, merge, or probabilistically use sequencing evidence often read PL (or log-scale GL) rather than hard Genotype calls alone.

Example usage

"We retained all sites but filtered sample genotypes using GQ derived from FORMAT PL."

Genotype Genotype likelihood Genotype quality (GQ) PL and GQ Phred quality score Ploidy Variant Call Format (VCF)
Related-term network

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Node order. The current term is first. Next come every page linked from Related terms, in the same top-to-bottom order as that list. Then new terms appear in two-hop layers: for each of those direct neighbors (in that same order), their related terms are appended if not already listed. A third pass does the same for two-hop nodes. The walk stops when a fixed maximum number of nodes is reached.

References

  • Danecek P, et al. (2021). Twelve years of SAMtools and BCFtools. Gigascience.
  • HTS specifications: VCF FORMAT PL. https://samtools.github.io/hts-specs/
← Phred quality score Phylogenetics →

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