Demo entry 6342774

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Submitted by anonymous on Jan 07, 2017 at 12:34
Language: Bash. Code size: 829 Bytes.

### CHRONOLOGY
### ALL COMMANDS/SCRIPTS PUT IN CHRONOLOGICAL ORDER
### LAST MODIFICATION: 28.06.2016


######### 1.Add modules
module add UHTS/Quality_control/Reapr/1.0.16;
module add UHTS/Analysis/vcflib/2014.10.17;
module add UHTS/Analysis/vcftools/0.1.12b;
module add UHTS/Analysis/plink/1.90;
#module add UHTS/Analysis/plink/1.07;
module add UHTS/Analysis/samtools/1.3;




######### 2. COPY ALL NECESSARY PLINK FILES FOR IMPUTATION TO TARGET DIRECTORY (+REMOVE THE 'MERGED' FILES)

# Copy all files from european ancestry
cp *eur* /data/epfl/fellay/fhodel/7_Imputation/1_PLINK2VCF/PLINK

# Remove unnecessary files
rm *merge* 

# List of filenames
ls -1 | sed -e 's/\..*$//'

# Rename files: remove '.qc'
for filename in ./*do
	mv "./$filename" "./$(echo $filename | sed -e 's/.qc//g')";
done

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