Local assembly and genotype likelihoods
Research context
research method · established · As of 2026-10-10
HaplotypeCaller assembles candidate haplotypes in active regions and compares reads with them through PairHMM likelihoods before genotype inference.
Key knowledge
HaplotypeCaller assembles candidate haplotypes in active regions and compares reads with them through PairHMM likelihoods before genotype inference. Read evidence depends on the error/alignment model, ploidy and candidate haplotypes; a call is an inferred genotype rather than directly observed sequence truth.
Conditions and scope
- Intermediate gVCFs are not final joint calls; the germline caller is not recommended for extreme-frequency somatic discovery.
Sources · 1
References
Sources retain their recorded scope. A source link alone does not establish verification of every statement.
Evidence and review
HaplotypeCaller: Active regions, local assembly, PairHMM likelihoods and genotyping limits (actual official method overview)
2026-10-10 · Bounded author source inspection of local assembly and genotype likelihoods, including the stated conditions; independent branch review is recorded separately.
Entry details
Permanent link to this entry ↗- Record identity
- res-bio-variant-likelihood
- Revision
- research.1
- Structured reference record
- Postgraduate & research reference