Here is the qualtrics link for this session
https://qimr.az1.qualtrics.com/jfe/form/SV_eA90nL27Ww43rIa




Here are the commands in a txt file if that is easier to work with

# Today we will be working in scratch today as the files we're using are big
mkdir -p /scratch/${USER}/{raw,mds,qc,saige}

# first we're going to copy the plink files we'll be using as input
cp /faculty/sarah/2023/Imputation/* /scratch/${USER}/saige/
mv /scratch/${USER}/saige/myers19.* /scratch/${USER}/raw/

#next we are going to start the singularity container
singularity shell --hostname localhost --bind /scratch/${USER}:/data /usr/local/lib/singularity/ImputationProtocol.sif

# and load the applications we'll be using 
setup-hadoop --n-cores 2
setup-imputationserver

# Next we're going to set up the files for imputation
# we start by make some MDS components (which are conceptually similar to PCs) 
# this is not technically part of an imputation protocol but it is good to check the ancestry of your sample before imputing
cd /data/mds
enigma-mds --bfile ../raw/myers19

# then we're going to do one final QC step
cd /data/qc
enigma-qc --bfile /data/raw/myers19 -c 19 --study-name myers19

# now we're going to start imputing
imputationserver --study-name myers19 --population eur

#OH NO!!! we have strand flips - luckily we can easily fix this
check flip --bfile ../raw/myers19

# we need to remake the vcf files  
cd /data/qc
enigma-qc --bfile /data/raw/myers19.check-flip -c 19 --study-name myers19

# then try the imputation again
imputationserver --study-name myers19 --population eur


########################################################################

#Once the imputation is finished we will exit the container and process the data
exit
cd /scratch/${USER}/output/myers19/local/

#Unzipping the data 
7za -ppassword x chr_19.zip
tabix -f -p vcf -C chr19.dose.vcf.gz

#########################################################################

#First we'll load SAIGE

singularity shell --hostname localhost --bind /scratch/${USER}:/data  /usr/local/lib/singularity/saige.sif
cd /data/saige

#Next we'll run step 1 of the SAIGE analysis in this step we run the LMM and creates a pre-processed r data file
 ./SAIGE_step1AD.sh

#Next we'll run step 2 of the SAIGE analysis in this step we run the association analyses
 ./SAIGE_step2AD.sh

exit

#########################################################################