From 79d19f4ce5cdce7f78128e8d7321dfa701e1d04b Mon Sep 17 00:00:00 2001
From: zsloan
Date: Sat, 28 Aug 2021 00:47:39 +0000
Subject: Fix issue that caused R/qtl to not use the first covariate when using
 stratified permutations + covariates

---
 scripts/rqtl_wrapper.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/rqtl_wrapper.R b/scripts/rqtl_wrapper.R
index f6788c5..7518175 100644
--- a/scripts/rqtl_wrapper.R
+++ b/scripts/rqtl_wrapper.R
@@ -167,7 +167,7 @@ if (!is.null(opt$addcovar)) {
   if (!is.null(opt$pstrata)) {
     covar_names = trait_names[3:length(trait_names) - 1]
   } else {
-    covar_names = trait_names[3:length(trait_names)]
+    covar_names = trait_names[2:length(trait_names)]
   }
   covars <- pull.pheno(cross_object, covar_names)
 }
-- 
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