CSF_QTL_ANALYSIS_Pipeline_May18_2017

CSF_QTLpipelin_SNPtest.sh

Wed 15 Feb 2017 04:06:05 PM PST 
#!/bin/sh
for i in `seq 1 22`
do
command=`echo snptest -data /srv/gsfs0/projects/mignot/hcrtgwas/CHR"$i".Plate86to87.impute2 /srv/gsfs0/projects/mignot/hcrtgwas/CHR"$i".86to87.updated.sample -method score -cov_names C1 C2 C3 C4 C5 C6 C7 C8 C9 -frequentist 1 -pheno HCRT -o hcrt.plate86to87updated.CHR"$i" -exclude_samples /srv/gsfs0/projects/mignot/hcrtgwas/CHR"$i".86to87.exclusion.sample`
touch tmpchr SNPtest.$i.sh
chmod 755 SNPtest.$i.sh
echo \#\!/bin/bash >SNPtest.$i.sh
echo \#$ -N chr"$i"_SNPtest >>SNPtest.$i.sh
echo \#$ -l h_vmem=5G >>SNPtest.$i.sh
echo \#$ -l h_rt=12:00:00 >>SNPtest.$i.sh
echo \#$ -w e >>SNPtest.$i.sh
echo "module add snptest/2.5-beta4" >>SNPtest.$i.sh
echo $command >> SNPtest.$i.sh

qsub -V -cwd SNPtest.$i.sh
done




##loop to create all sample files for SNPtest
#!/bin/sh
for i in `seq 1 604`
do 
	awk -v i="$i" '{print$i}' csf_vars_phenofinal > temp_ph_"$i"
	for j in `seq 1 22`
	do
		paste -d" " /media/labcomp/HDD/GWASProjects/batch2_jan25/HCRTSNPtest/CHR"$j".86to87.updated.sample temp_ph_"$i" > /media/labcomp/HDD/GWASProjects/batch2_jan25/CSFQTLS/SNPtest_construct/CHR"$j".86to87.ph_"$i".sample
	done
done

##do a local SNP test to see if the cluster picks it up
snptest_v2.5.2 -data /media/labcomp/HDD/GWASProjects/batch2_jan25/imputed_files/CHR1.Plate86to87.impute2 \
/media/labcomp/HDD/GWASProjects/batch2_jan25/CSFQTLS/SNPtest_construct/CHR1.86to87.ph_1.sample \
-method score \
-cov_names C1 C2 C3 C4 C5 C6 C7 C8 C9 gender Age BMI \
-frequentist 1 \
-pheno Ph_1 \
-o test_chr1.ph1 
-printids


##parallel bash commands
parallel --jobs 8 awk -v i={} '{print$i}' csf_vars_phenofinal '>' /media/labcomp/HDD/GWASProjects/temp_ph{} ::: {1..604}

parallel --jobs 8 snptest_v2.5.2 -data /media/labcomp/HDD/GWASProjects/batch2_jan25/imputed_files/CHR"$i".Plate86to87.impute2 /media/labcomp/HDD/GWASProjects/batch2_jan25/CSFQTLS/SNPtest_construct/CHR"$i".86to87.ph_1.sample -method score -cov_names C1 C2 C3 C4 C5 C6 C7 C8 C9 gender Age BMI -frequentist 1 -pheno Ph_1 -o CSFq_chr"$i".ph1 




parallel --jobs 8 ./ph1_snptest.{}.sh '>' temp{} ::: {1..22}


watch -n5 tail -n1 temp_*


for j in `seq 2 604`
do 
	for i in `seq 1 22`
	do 
	touch ph"$j"_snptest.$i.sh
	chmod 777 ph"$j"_snptest.$i.sh
	echo \#\!/bin/bash >> ph"$j"_snptest.$i.sh
	echo \snptest_v2.5.2 -data /media/labcomp/HDD/GWASProjects/batch2_jan25/imputed_files/CHR"$i".Plate86to87.impute2 /media/labcomp/HDD/GWASProjects/batch2_jan25/CSFQTLS/SNPtest_construct/CHR"$i".86to87.ph_"$j".sample -method score -cov_names C1 C2 C3 C4 C5 C6 C7 C8 C9 gender Age BMI -frequentist 1 -pheno Ph_"$j" -o CSFq_chr"$i".ph"$j" >> ph"$j"_snptest.$i.sh
	done
done

for i in `seq 81 120`
do
parallel --jobs 16  ./ph"$i"_snptest.{}.sh '>' temp_"$i"_{} ::: {1..22}
done


scp ambati@scg4.stanford.edu:/srv/gsfs0/projects/mignot/hcrtgwas/Plate86and87PMRAv1* /media/labcomp/HDD/GWASProjects/batch2_jan25
scp /media/labcomp/HDD/GWASProjects/batch2_jan25/CSFQTLS/SNPtest_construct/*.sample ambati@scg4.stanford.edu:/srv/gsfs0/projects/mignot/hcrtgwas/csfqtl

plate86to87clusterdata
##implment SNPtest on the cluster 
##datamover nodes

scp/media/labcomp/HDD/GWASProjects/batch2_jan25/imputed_files/*.impute2 ambati@mignot-sleep-app-01.stanford.edu:/home/ambati/GWAS




rsync -av --progress ambati@scg4-dtn02:/srv/gsfs0/projects/mignot/hcrtgwas/csfqtl/cat_ph{1..604} /media/labcomp/HDD2/CSFqtls_SNPtest/


#on the sleep server
#!/bin/sh
for j in `seq 1 604`
do
  	for i in `seq 1 22`
        do
	touch ph"$j"_snptest.$i.sh
        chmod 777 ph"$j"_snptest.$i.sh
        echo \#\!/bin/bash >> ph"$j"_snptest.$i.sh
        echo \./snptest_v2.5.2 -data /home/ambati/GWAS/CHR"$i".Plate86to87.impute2 /home/ambati/GWAS/CHR"$i".86to87.ph_"$j".sample -method score -cov_names C1 C2 C3 C4 C5 C6 C7 C8 C9 gender Age BMI -frequentist 1 -pheno Ph_"$j" -o CSFq_chr"$i".ph"$j" >> ph"$j"_snptest.$i.sh
	done
done





















##bayesian quant 
snptest_v2.5.2 -data /media/labcomp/HDD/GWASProjects/batch2_jan25/imputed_files/CHR1.Plate86to87.impute2 \
/media/labcomp/HDD/GWASProjects/batch2_jan25/CSFQTLS/SNPtest_construct/CHR1.86to87.ph_1.sample \
-method expected \
-cov_names C1 C2 C3 C4 C5 C6 C7 C8 C9 gender Age BMI \
-bayesian 1 \
-pheno Pheno_x  \
-o test_chr1.ph1 \
-prior_qt_mean_b 0 \
-prior_qt_V_b 0.02 \
-prior_qt_a 3 \
-prior_qt_b 2