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Callable genome

Definition
AI-generated

The callable genome is the subset of a reference assembly where a pipeline can confidently call genotypes given depth, mapping quality, and mappability filters.

Topics
Sequencing Data Analysis
Related
Blacklisted region Breadth of coverage Callability

Why it matters in GWAS

Association and burden analyses should align variant sets and masks with the callable fraction to avoid interpreting missing calls as true absence, especially for WGS versus array imputation comparisons.

Example usage

"The callable genome mask excluded high-repeat regions before burden tests."

Blacklisted region Breadth of coverage Callability Mappability
Related-term network

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References

  • Zook JM, et al. (2019). A robust benchmark for detection of germline large deletions and insertions. Nat Biotechnol.
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