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Joint genotyping

Definition
AI-generated

Joint genotyping combines evidence across samples at each site—often from gVCFs—to produce a cohort VCF with consistent posteriors and allele frequencies, rather than calling each sample in isolation.

Topics
Sequencing Data Analysis
Related
Cohort call set Genome Analysis Toolkit (GATK) GenomicsDB

Why it matters in GWAS

Joint calling improves sensitivity for low-frequency variants and harmonizes filters across studies, supporting multi-cohort WGS meta-analyses and rare-variant tests.

Example usage

"Joint genotyping was performed with GATK HaplotypeCaller in GVCF mode followed by GenomicsDBImport."

Cohort call set Genome Analysis Toolkit (GATK) GenomicsDB Genotype likelihood HaplotypeCaller Variant Calling
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

  • Poplin R, et al. (2017). Scaling accurate genetic variant discovery to tens of thousands of samples. bioRxiv (GATK).
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