diff --git a/script/geno_prep/plink.sh b/script/geno_prep/plink.sh index 94025cb..d659bf0 100755 --- 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"