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Hard filtering

Definition
AI-generated

Hard filtering removes variants or genotypes by fixed rules on annotations such as depth, strand bias, or quality without a learned model—contrasted with machine-learned recalibration (for example VQSR).

Topics
Sequencing Data Analysis
Related
Site-level filter Variant Quality Score Recalibration (VQSR)

Why it matters in GWAS

Transparent hard filters aid reproducibility in rare-variant studies where training data for VQSR may be sparse.

Example usage

"Hard filtering on QD and FS removed indels before gene-based tests."

Site-level filter Variant Quality Score Recalibration (VQSR)
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.
← Hard clipping Hardy-Weinberg Equilibrium (HWE) →

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