From 69805861a87db8274731febd8d005c480c96aa24 Mon Sep 17 00:00:00 2001
From: tj <tjzhao@ucdavis.edu>
Date: Fri, 18 Mar 2022 10:48:30 -0700
Subject: [PATCH] update GWAS() to remove extra snps in user's mapfile

---
 src/3.GWAS/src/GWAS.jl | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/src/3.GWAS/src/GWAS.jl b/src/3.GWAS/src/GWAS.jl
index 1d2ac9cc..2efbcd1c 100644
--- 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])