update GWAS() to remove extra snps in user's mapfile

reworkhow · Mar 18, 2022 · 6980586 · 6980586
1 parent 95852dc
commit 6980586
Showing 1 changed file with 5 additions and 0 deletions.
diff --git a/src/3.GWAS/src/GWAS.jl b/src/3.GWAS/src/GWAS.jl
@@ -77,6 +77,11 @@ function GWAS(mme,map_file,marker_effects_file::AbstractString...;
 
     window_size_bp = map(Int64,parse(Float64,split(window_size)[1])*1_000_000)
     mapfile = (header == true ? readdlm(map_file,',',header=true)[1] : readdlm(map_file,','))
+    #remove SNPs in mapfile that are not used in Bayesian analysis (e.g., removed in QC)
+    snpID    = mme.M[1].markerID
+    in_snpID = findall(x -> x ∈ snpID, mapfile[:,1])
+    mapfile  = mapfile[in_snpID,:]
+
     chr     = map(string,mapfile[:,2])
     pos     = map(Int64,mapfile[:,3])