Update plink.sh

jiang548 · May 20, 2022 · 492cba9 · 492cba9
1 parent 89cc69c
commit 492cba9
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/script/geno_prep/plink.sh b/script/geno_prep/plink.sh
@@ -1,9 +1,9 @@
 ## This sciprt will apply plink commands to the files
 
-echo -e "Preprocessing using Plink ...\n"
+echo -e "Preprocessing genotype data with PLINK...\n"
 
 plink --silent --noweb --ped $pedfile --map $mapfile --geno $geno --hwe $hwe --recode --snps-only --list-duplicate-vars suppress-first --out $SIGNET_TMP_ROOT/tmpg/clean_Genotype &&
 plink --silent --noweb --file $SIGNET_TMP_ROOT/tmpg/clean_Genotype --mind $mind --exclude $SIGNET_TMP_ROOT/tmpg/clean_Genotype.dupvar --recode --out $SIGNET_TMP_ROOT/tmpg/clean_Genotype --set-hh-missing &&
 plink --silent --noweb --file $SIGNET_TMP_ROOT/tmpg/clean_Genotype --recodeA --out $SIGNET_TMP_ROOT/tmpg/clean_Genotype --set-hh-missing &&
 tail -n+2 $SIGNET_TMP_ROOT/tmpg/clean_Genotype.raw > $SIGNET_TMP_ROOT/tmpg/clean_Genotype.data  &&
-echo -e "Plink preprocessing finished\n"
+echo -e "Preprocessing genotype data... Completed!\n"