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Site-level filter

Definition
AI-generated

A site-level filter flags a variant as low quality for all samples together (for example FS, QD, InbreedingCoeff), independent of individual genotype uncertainty.

Topics
Sequencing Data Analysis
Related
Genotype-level filter Hard filtering

Why it matters in GWAS

Site filters define which rows enter association; they differ from genotype-level filters that vary by person.

Example usage

"The VCF listed site-level filter status in FILTER, retaining PASS variants only."

Genotype-level filter Hard filtering
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

  • Van der Auwera GA, et al. (2013). From FastQ data to high-confidence variant calls. Curr Protoc Bioinformatics.
← Site frequency spectrum Sequence Kernel Association Test (SKAT) →

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