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Variant Missingness

Definition
AI-generated

Variant missingness is the fraction of samples lacking a genotype call for a given SNP or variant.

Topics
GWAS
Related
Call Rate Differential Missingness Quality Control (QC)

Why it matters in GWAS

Variants with high missingness are more likely to reflect assay problems or batch artifacts and can bias downstream association tests or imputation.

Example usage

"SNPs with variant missingness above 1% were filtered out during pre-imputation QC."

Call Rate Differential Missingness Quality Control (QC) Sample Missingness
Related-term network

Click any node to open that term page.

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

  • Anderson CA, et al. (2010). Data quality control in genetic case-control association studies. Nat Protoc.
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