Farmacogenetics pipeline
Preprocessing steps: 1: convert idat to gtc 2: create new folder in /groups/umcg-pgx/tmp07/rawdata/hematologie_research_data (e.g. Jackie-Augustus) 3: create a subfolder GTC folder 4: copy data to Jackie-Augustus (this will be original data) 5: create a new folder (on the level of Jackie-Augustus) called Jackie-Augustus_plusGDIO (this will be a combination of possibly multiple gtc data) 6: go in the Jackie-Augustus_plusGDIO folder and do following command: ln -s ../Jackie-Augustus/* . 7: still in GTC folder run this command: ln -s ../../GDIO/GTC/* . 8: combine samplesheets of GDIO (/groups/umcg-pgx/tmp07/rawdata/GDIO/GTC/GDIO.csv), with the analysing samples samplesheet, be aware of mismatching columns
PROJECT=e.g. Jackie-Augustus_plusGDIO SAMPLESHEET= e.g. Jackie-Augustus_plusGDIO.csv
mkdir /groups/umcg-pgx/tmp07/generatedscripts/{PROJECT}
module load PGx
cp ${EBROOTPGX}/generate_template.sh /groups/umcg-pgx/tmp07/generatedscripts/{PROJECT}/
cp SAMPLESHEET /groups/umcg-pgx/tmp07/generatedscripts/{PROJECT}/
bash generate_template.sh
bash submit.sh