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modified: cisQTLAnalyzer.sh
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@jaccoschaap
jaccoschaap committed Oct 25, 2017
1 parent 5c80c2f commit b641c92
Showing 1 changed file with 4 additions and 4 deletions.
8 changes: 4 additions & 4 deletions cisQTLAnalyzer.sh
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Expand Up @@ -1058,26 +1058,26 @@ else
echo "Creating bash-script to submit nominal pass with the clumped dataset for 'cis-eQTLs'..."
### FOR DEBUGGING
###${FASTQTL} --vcf ${REGIONALDIR}/${SNPTESTOUTPUTDATA}_QC_${VARIANT}_excl_${EXCLUSION_TYPE}.vcf.gz --bed ${FASTQTLDATA} --region 0${CHR}:${START}-${END} --seed ${SEEDNO} --window ${WINDOWSIZE} --exclude-samples ${EXCLUSION_LIST} --exclude-covariates ${EXCLUSION_COV} --cov ${COVARIATES} --out ${REGIONALDIR}/${STUDYNAME}_QC_qtlnom_${VARIANT}_excl_${EXCLUSION_TYPE}.txt.gz --log ${REGIONALDIR}/${STUDYNAME}_QC_qtlnom_${VARIANT}_excl_${EXCLUSION_TYPE}.log
echo "${QTL} cis --vcf ${REGIONALDIR}/${SNPTESTOUTPUTDATA}_QC_${VARIANT}_excl_${EXCLUSION_TYPE}.vcf.gz --bed ${FASTQTLDATA} --region 0${CHR}:${START}-${END} --seed ${SEEDNO} --window ${WINDOWSIZE} --nominal 1e-5 --exclude-samples ${EXCLUSION_LIST} --exclude-covariates ${EXCLUSION_COV} --cov ${COVARIATES} --include-sites ${CLUMPDIR}/only_ldbuddies_${VARIANT}.list --out ${REGIONALDIR}/${STUDYNAME}_QC_qtlnom_clumped_${VARIANT}_excl_${EXCLUSION_TYPE}.txt.gz --log ${REGIONALDIR}/${STUDYNAME}_QC_qtlnom_clumped${VARIANT}_excl_${EXCLUSION_TYPE}.log "> ${REGIONALDIR}/${STUDYNAME}_QC_qtlnom_clumped_${VARIANT}_excl_${EXCLUSION_TYPE}_NOM.sh
echo "${QTL} cis --vcf ${REGIONALDIR}/${SNPTESTOUTPUTDATA}_QC_${VARIANT}_excl_${EXCLUSION_TYPE}.vcf.gz --bed ${FASTQTLDATA} --region 0${CHR}:${START}-${END} --seed ${SEEDNO} --window ${WINDOWSIZE} --nominal 1e-5 --exclude-samples ${EXCLUSION_LIST} --exclude-covariates ${EXCLUSION_COV} --cov ${COVARIATES} --include-sites ${CLUMPDIR}/only_ldbuddies_${VARIANT}.list --out ${REGIONALDIR}/${STUDYNAME}_QC_qtlnom_clumped_${VARIANT}_excl_${EXCLUSION_TYPE}.txt.gz --log ${REGIONALDIR}/${STUDYNAME}_QC_qtlnom_clumped$_{VARIANT}_excl_${EXCLUSION_TYPE}.log "> ${REGIONALDIR}/${STUDYNAME}_QC_qtlnom_clumped_${VARIANT}_excl_${EXCLUSION_TYPE}_NOM.sh
qsub -S /bin/bash -N QTL_${STUDYJOBNAME}_clumped_excl_${EXCLUSION_TYPE}_${PROJECTNAME} -hold_jid CLUMP_${STUDYJOBNAME}_excl_${EXCLUSION_TYPE}_${PROJECTNAME} -e ${REGIONALDIR}/${STUDYNAME}_QC_qtlnom_${VARIANT}_excl_${EXCLUSION_TYPE}_NOM.errors -o ${REGIONALDIR}/${STUDYNAME}_QC_qtlnom_${VARIANT}_excl_${EXCLUSION_TYPE}_NOM.output -l h_rt=${QUEUE_NOM} -l h_vmem=${VMEM_NOM} -M ${EMAIL} -m ${MAILTYPE} -wd ${REGIONALDIR} ${REGIONALDIR}/${STUDYNAME}_QC_qtlnom_clumped_${VARIANT}_excl_${EXCLUSION_TYPE}_NOM.sh
echo "Creating bash-script to submit permutation pass for 'cis-eQTLs'..."
### FOR DEBUGGING
###${FASTQTL} --vcf ${REGIONALDIR}/${SNPTESTOUTPUTDATA}_QC_${VARIANT}_excl_${EXCLUSION_TYPE}.vcf.gz --bed ${FASTQTLDATA} --region 0${CHR}:${START}-${END} --seed ${SEEDNO} --window ${WINDOWSIZE} --permute ${PERMSTART} ${PERMEND} --exclude-samples ${EXCLUSION_LIST} --exclude-covariates ${EXCLUSION_COV} --cov ${COVARIATES} --out ${REGIONALDIR}/${STUDYNAME}_QC_qtlperm_${VARIANT}_excl_${EXCLUSION_TYPE}.txt.gz --log ${REGIONALDIR}/${STUDYNAME}_QC_qtlperm_${VARIANT}_excl_${EXCLUSION_TYPE}.log
echo "${QTL} cis --vcf ${REGIONALDIR}/${SNPTESTOUTPUTDATA}_QC_${VARIANT}_excl_${EXCLUSION_TYPE}.vcf.gz --bed ${FASTQTLDATA} --region 0${CHR}:${START}-${END} --seed ${SEEDNO} --window ${WINDOWSIZE} --permute ${PERMSTART} ${PERMEND} --exclude-samples ${EXCLUSION_LIST} --exclude-covariates ${EXCLUSION_COV} --cov ${COVARIATES} --include-sites ${CLUMPDIR}/only_ldbuddies_${VARIANT}.list --out ${REGIONALDIR}/${STUDYNAME}_QC_qtlperm_clumped_${VARIANT}_excl_${EXCLUSION_TYPE}.txt.gz --log ${REGIONALDIR}/${STUDYNAME}_QC_qtlperm_clumped${VARIANT}_excl_${EXCLUSION_TYPE}.log "> ${REGIONALDIR}/${STUDYNAME}_QC_qtlperm_clumped_${VARIANT}_excl_${EXCLUSION_TYPE}_PERMUTE.sh
echo "${QTL} cis --vcf ${REGIONALDIR}/${SNPTESTOUTPUTDATA}_QC_${VARIANT}_excl_${EXCLUSION_TYPE}.vcf.gz --bed ${FASTQTLDATA} --region 0${CHR}:${START}-${END} --seed ${SEEDNO} --window ${WINDOWSIZE} --permute ${PERMSTART} ${PERMEND} --exclude-samples ${EXCLUSION_LIST} --exclude-covariates ${EXCLUSION_COV} --cov ${COVARIATES} --include-sites ${CLUMPDIR}/only_ldbuddies_${VARIANT}.list --out ${REGIONALDIR}/${STUDYNAME}_QC_qtlperm_clumped_${VARIANT}_excl_${EXCLUSION_TYPE}.txt.gz --log ${REGIONALDIR}/${STUDYNAME}_QC_qtlperm_clumped_${VARIANT}_excl_${EXCLUSION_TYPE}.log "> ${REGIONALDIR}/${STUDYNAME}_QC_qtlperm_clumped_${VARIANT}_excl_${EXCLUSION_TYPE}_PERMUTE.sh
qsub -S /bin/bash -N QTL_${STUDYJOBNAME}_clumped_excl_${EXCLUSION_TYPE}_${PROJECTNAME} -hold_jid CLUMP_${STUDYJOBNAME}_excl_${EXCLUSION_TYPE}_${PROJECTNAME} -e ${REGIONALDIR}/${STUDYNAME}_QC_qtlperm_${VARIANT}_excl_${EXCLUSION_TYPE}_PERMUTE.errors -o ${REGIONALDIR}/${STUDYNAME}_QC_qtlperm_${VARIANT}_excl_${EXCLUSION_TYPE}_PERMUTE.output -l h_rt=${QUEUE_PERM} -l h_vmem=${VMEM_PERM} -M ${EMAIL} -m ${MAILTYPE} -wd ${REGIONALDIR} ${REGIONALDIR}/${STUDYNAME}_QC_qtlperm_clumped_${VARIANT}_excl_${EXCLUSION_TYPE}_PERMUTE.sh
elif [[ ${CHR} -ge 10 ]]; then
echo "Processing a variant in clumped region ${CHR}:${START}-${END}."
###Running nominal and permutation passes of fastQTL, respectively
echo "Creating bash-script to submit nominal pass for 'cis-eQTLs'..."
### FOR DEBUGGING
###${FASTQTL} --vcf ${REGIONALDIR}/${SNPTESTOUTPUTDATA}_QC_${VARIANT}_excl_${EXCLUSION_TYPE}.vcf.gz --bed ${FASTQTLDATA} --region ${CHR}:${START}-${END} --seed ${SEEDNO} --window ${WINDOWSIZE} --exclude-samples ${EXCLUSION_LIST} --exclude-covariates ${EXCLUSION_COV} --cov ${COVARIATES} --out ${REGIONALDIR}/${STUDYNAME}_QC_qtlnom_${VARIANT}_excl_${EXCLUSION_TYPE}.txt.gz --log ${REGIONALDIR}/${STUDYNAME}_QC_qtlnom_${VARIANT}_excl_${EXCLUSION_TYPE}.log
echo "${QTL} cis --vcf ${REGIONALDIR}/${SNPTESTOUTPUTDATA}_QC_${VARIANT}_excl_${EXCLUSION_TYPE}.vcf.gz --bed ${FASTQTLDATA} --region ${CHR}:${START}-${END} --seed ${SEEDNO} --window ${WINDOWSIZE} --nominal 1e-5 --exclude-samples ${EXCLUSION_LIST} --exclude-covariates ${EXCLUSION_COV} --cov ${COVARIATES} --include-sites ${CLUMPDIR}/only_ldbuddies_${VARIANT}.list --out ${REGIONALDIR}/${STUDYNAME}_QC_qtlnom_clumped_${VARIANT}_excl_${EXCLUSION_TYPE}.txt.gz --log ${REGIONALDIR}/${STUDYNAME}_QC_qtlnom_clumped${VARIANT}_excl_${EXCLUSION_TYPE}.log "> ${REGIONALDIR}/${STUDYNAME}_QC_qtlnom_clumped_${VARIANT}_excl_${EXCLUSION_TYPE}_NOM.sh
echo "${QTL} cis --vcf ${REGIONALDIR}/${SNPTESTOUTPUTDATA}_QC_${VARIANT}_excl_${EXCLUSION_TYPE}.vcf.gz --bed ${FASTQTLDATA} --region ${CHR}:${START}-${END} --seed ${SEEDNO} --window ${WINDOWSIZE} --nominal 1e-5 --exclude-samples ${EXCLUSION_LIST} --exclude-covariates ${EXCLUSION_COV} --cov ${COVARIATES} --include-sites ${CLUMPDIR}/only_ldbuddies_${VARIANT}.list --out ${REGIONALDIR}/${STUDYNAME}_QC_qtlnom_clumped_${VARIANT}_excl_${EXCLUSION_TYPE}.txt.gz --log ${REGIONALDIR}/${STUDYNAME}_QC_qtlnom_clumped_${VARIANT}_excl_${EXCLUSION_TYPE}.log "> ${REGIONALDIR}/${STUDYNAME}_QC_qtlnom_clumped_${VARIANT}_excl_${EXCLUSION_TYPE}_NOM.sh
qsub -S /bin/bash -N QTL_${STUDYJOBNAME}_clumped_excl_${EXCLUSION_TYPE}_${PROJECTNAME} -hold_jid CLUMP_${STUDYJOBNAME}_excl_${EXCLUSION_TYPE}_${PROJECTNAME} -e ${REGIONALDIR}/${STUDYNAME}_QC_qtlnom_${VARIANT}_excl_${EXCLUSION_TYPE}_NOM.errors -o ${REGIONALDIR}/${STUDYNAME}_QC_qtlnom_${VARIANT}_excl_${EXCLUSION_TYPE}_NOM.output -l h_rt=${QUEUE_NOM} -l h_vmem=${VMEM_NOM} -M ${EMAIL} -m ${MAILTYPE} -wd ${REGIONALDIR} ${REGIONALDIR}/${STUDYNAME}_QC_qtlnom_clumped_${VARIANT}_excl_${EXCLUSION_TYPE}_NOM.sh
echo ""
echo "Creating bash-script to submit permutation pass with the clumped dataset for 'cis-eQTLs'..."
### FOR DEBUGGING
###${FASTQTL} --vcf ${REGIONALDIR}/${SNPTESTOUTPUTDATA}_QC_${VARIANT}_excl_${EXCLUSION_TYPE}.vcf.gz --bed ${FASTQTLDATA} --region ${CHR}:${START}-${END} --seed ${SEEDNO} --window ${WINDOWSIZE} --permute ${PERMSTART} ${PERMEND} --exclude-samples ${EXCLUSION_LIST} --exclude-covariates ${EXCLUSION_COV} --cov ${COVARIATES} --out ${REGIONALDIR}/${STUDYNAME}_QC_qtlperm_${VARIANT}_excl_${EXCLUSION_TYPE}.txt.gz --log ${REGIONALDIR}/${STUDYNAME}_QC_qtlperm_${VARIANT}_excl_${EXCLUSION_TYPE}.log
echo "${QTL} cis --vcf ${REGIONALDIR}/${SNPTESTOUTPUTDATA}_QC_${VARIANT}_excl_${EXCLUSION_TYPE}.vcf.gz --bed ${FASTQTLDATA} --region ${CHR}:${START}-${END} --seed ${SEEDNO} --window ${WINDOWSIZE} --permute ${PERMSTART} ${PERMEND} --exclude-samples ${EXCLUSION_LIST} --exclude-covariates ${EXCLUSION_COV} --cov ${COVARIATES} --include-sites ${CLUMPDIR}/only_ldbuddies_${VARIANT}.list --out ${REGIONALDIR}/${STUDYNAME}_QC_qtlperm_clumped_${VARIANT}_excl_${EXCLUSION_TYPE}.txt.gz --log ${REGIONALDIR}/${STUDYNAME}_QC_qtlperm_clumped${VARIANT}_excl_${EXCLUSION_TYPE}.log "> ${REGIONALDIR}/${STUDYNAME}_QC_qtlperm_clumped_${VARIANT}_excl_${EXCLUSION_TYPE}_PERMUTE.sh
echo "${QTL} cis --vcf ${REGIONALDIR}/${SNPTESTOUTPUTDATA}_QC_${VARIANT}_excl_${EXCLUSION_TYPE}.vcf.gz --bed ${FASTQTLDATA} --region ${CHR}:${START}-${END} --seed ${SEEDNO} --window ${WINDOWSIZE} --permute ${PERMSTART} ${PERMEND} --exclude-samples ${EXCLUSION_LIST} --exclude-covariates ${EXCLUSION_COV} --cov ${COVARIATES} --include-sites ${CLUMPDIR}/only_ldbuddies_${VARIANT}.list --out ${REGIONALDIR}/${STUDYNAME}_QC_qtlperm_clumped_${VARIANT}_excl_${EXCLUSION_TYPE}.txt.gz --log ${REGIONALDIR}/${STUDYNAME}_QC_qtlperm_clumped_${VARIANT}_excl_${EXCLUSION_TYPE}.log "> ${REGIONALDIR}/${STUDYNAME}_QC_qtlperm_clumped_${VARIANT}_excl_${EXCLUSION_TYPE}_PERMUTE.sh
qsub -S /bin/bash -N QTL_${STUDYJOBNAME}_clumped_excl_${EXCLUSION_TYPE}_${PROJECTNAME} -hold_jid CLUMP_${STUDYJOBNAME}_excl_${EXCLUSION_TYPE}_${PROJECTNAME} -e ${REGIONALDIR}/${STUDYNAME}_QC_qtlperm_${VARIANT}_excl_${EXCLUSION_TYPE}_PERMUTE.errors -o ${REGIONALDIR}/${STUDYNAME}_QC_qtlperm_${VARIANT}_excl_${EXCLUSION_TYPE}_PERMUTE.output -l h_rt=${QUEUE_PERM} -l h_vmem=${VMEM_PERM} -M ${EMAIL} -m ${MAILTYPE} -wd ${REGIONALDIR} ${REGIONALDIR}/${STUDYNAME}_QC_qtlperm_clumped_${VARIANT}_excl_${EXCLUSION_TYPE}_PERMUTE.sh
else
echo "*** ERROR *** Something is rotten in the City of Gotham; most likely a typo. Double back, please."
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