GWAS Quality Control: Call Rate Heterozygosity HWE and Sample Filters

Practical QC checklist; grounds the floor nodes (HWE, MAF) in a decision.

Questions this Concept answers

Why is a Hardy-Weinberg equilibrium (HWE) test applied to controls as a quality control step in a GWAS?

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Genome-Wide Association Study Workflow for Detecting Disease-Associated Loci Using PLINK

A genome-wide association study (GWAS) is a statistical method that scans millions of genetic variants (single nucleotide polymorphisms, SNPs) across the genomes of large cohorts to identify which va…