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"