Bio Workflows Gwas Pipeline

Orchestrates the GWAS pipeline from genotypes to association results, chaining PLINK2 QC (variant-then-sample missingness, controls-only HWE, KING relatedness), panel harmonization + joint phasing/imputation to dosages, long-range-LD-excluded PCA, and an engine chosen by sample structure (PLINK2-GLM / regenie / SAIGE / BOLT-LMM), with LDSC-intercept diagnostics. Use when committing the genome build + ancestry-matched imputation panel once (ancestry match > panel size), running the strand/allele harmonization gate (drop intermediate-frequency palindromes), imputing cases+controls TOGETHER on dosages, excluding long-range-LD regions before PCA, choosing an LMM when relatedn…