From 78ce6620985afb4dc4b34bdadcfc5d9e0bd4d718 Mon Sep 17 00:00:00 2001
From: "Zhang, Dabao" <zhangdb@purdue.edu>
Date: Fri, 20 May 2022 13:29:20 -0400
Subject: [PATCH] Update plink_gtex.sh

---
 script/geno_prep/plink_gtex.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/script/geno_prep/plink_gtex.sh b/script/geno_prep/plink_gtex.sh
index 0d184d9..50736d5 100755
--- a/script/geno_prep/plink_gtex.sh
+++ b/script/geno_prep/plink_gtex.sh
@@ -2,7 +2,7 @@
 
 cd $SIGNET_TMP_ROOT/tmpg
 
-echo -e "Preprocessing using Plink ...\n"
+echo -e "Preprocessing genotype data with PLINK...\n"
 
 plink --vcf GTEx_snp.vcf --double-id --make-bed --missing --freq --recode --out Geno_GTEx_$tissue
 plink --bfile Geno_GTEx_$tissue --recodeA --mac 5 --out GTEx_$tissue
@@ -15,4 +15,4 @@ awk {'print $5'} GTEx_$tissue.frq | tail -n+2 > ${resg}_snps.maf
 tail -n+2 GTEx_$tissue.raw |cut -d " " -f 7- > clean_Genotype.data
 sed -e 's/NA/0/g' clean_Genotype.data > ${resg}_clean_Genotype_repNA.data
 
-echo -e "Plink preprocessing finished\n"
+echo -e "Preprocessing genotype data ... completed!\n"