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Edits and bugs zapped.
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@swvanderlaan
swvanderlaan committed Jul 27, 2018
1 parent 826bf16 commit 1c06d99
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22 changes: 11 additions & 11 deletions QTLAnalyzer.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -98,8 +98,8 @@ echobold "+
echobold "+ +"
echobold "+ * Written by : Sander W. van der Laan; Jacco Schaap +"
echobold "+ * E-mail : s.w.vanderlaan-2@umcutrecht.nl; jacco_schaap@hotmail.com +"
echobold "+ * Last update : 2018-07-26 +"
echobold "+ * Version : 2.6.3 +"
echobold "+ * Last update : 2018-07-27 +"
echobold "+ * Version : 2.6.4 +"
echobold "+ +"
echobold "+ * Description : This script will set some directories, and execute a cis- or -trans-QTL analysis +"
echobold "+ according to your specifications and using your methylation or expression data. +"
Expand Down Expand Up @@ -379,20 +379,20 @@ else
### Note: this is also a quickfix given the new version of bgen2-format.
if [ ${CHR} -lt 10 ]; then
### FOR DEBUGGING
### ${QCTOOL2} -g ${GENETICDATA}/${SNPTESTDATA}${CHR}.bgen -s ${GENETICDATA}/${SNPTESTDATA}${CHR}.sample -excl-samples ${EXCLUSION_LIST} -og ${REGIONALDIR}/${SNPTESTOUTPUTDATA}_RAW_${VARIANT}_excl_${EXCLUSION_TYPE}.gen.gz -os ${REGIONALDIR}/${SNPTESTOUTPUTDATA}_RAW_${VARIANT}_excl_${EXCLUSION_TYPE}.sample -incl-range 0${CHR}:${START}-${END}
echo "${QCTOOL2} -g ${GENETICDATA}/${SNPTESTDATA}${CHR}.bgen -s ${GENETICDATA}/${SNPTESTDATA}${CHR}.sample -excl-samples ${EXCLUSION_LIST} -og ${REGIONALDIR}/${SNPTESTOUTPUTDATA}_RAW_${VARIANT}_excl_${EXCLUSION_TYPE}.gen.gz -os ${REGIONALDIR}/${SNPTESTOUTPUTDATA}_RAW_${VARIANT}_excl_${EXCLUSION_TYPE}.sample -incl-range 0${CHR}:${START}-${END} " > ${REGIONALDIR}/${STUDYNAME}_genex_${VARIANT}_excl_${EXCLUSION_TYPE}.sh
### ${QCTOOL} -g ${GENETICDATA}/${SNPTESTDATA}${CHR}.bgen -s ${GENETICDATA}/${SNPTESTDATA}${CHR}.sample -excl-samples ${EXCLUSION_LIST} -og ${REGIONALDIR}/${SNPTESTOUTPUTDATA}_RAW_${VARIANT}_excl_${EXCLUSION_TYPE}.gen.gz -os ${REGIONALDIR}/${SNPTESTOUTPUTDATA}_RAW_${VARIANT}_excl_${EXCLUSION_TYPE}.sample -incl-range 0${CHR}:${START}-${END}
echo "${QCTOOL} -g ${GENETICDATA}/${SNPTESTDATA}${CHR}.bgen -s ${GENETICDATA}/${SNPTESTDATA}${CHR}.sample -excl-samples ${EXCLUSION_LIST} -og ${REGIONALDIR}/${SNPTESTOUTPUTDATA}_RAW_${VARIANT}_excl_${EXCLUSION_TYPE}.gen.gz -os ${REGIONALDIR}/${SNPTESTOUTPUTDATA}_RAW_${VARIANT}_excl_${EXCLUSION_TYPE}.sample -incl-range 0${CHR}:${START}-${END} " > ${REGIONALDIR}/${STUDYNAME}_genex_${VARIANT}_excl_${EXCLUSION_TYPE}.sh
qsub -S /bin/bash -N GENEX${STUDYJOBNAME}_${VARIANT}_excl_${EXCLUSION_TYPE}_${PROJECTNAME} -e ${REGIONALDIR}/${STUDYNAME}_genex_${VARIANT}_excl_${EXCLUSION_TYPE}.errors -o ${REGIONALDIR}/${STUDYNAME}_genex_${VARIANT}_excl_${EXCLUSION_TYPE}.log -l h_rt=${QUEUE_QCTOOL} -l h_vmem=${VMEM_QCTOOL} -M ${EMAIL} -m ${MAILTYPE} -wd ${REGIONALDIR} ${REGIONALDIR}/${STUDYNAME}_genex_${VARIANT}_excl_${EXCLUSION_TYPE}.sh

elif [ ${CHR} -ge 10 ]; then
### FOR DEBUGGING
### ${QCTOOL2} -g ${GENETICDATA}/${SNPTESTDATA}${CHR}.bgen -s ${GENETICDATA}/${SNPTESTDATA}${CHR}.sample -excl-samples ${EXCLUSION_LIST} -og ${REGIONALDIR}/${SNPTESTOUTPUTDATA}_RAW_${VARIANT}_excl_${EXCLUSION_TYPE}.gen.gz -os ${REGIONALDIR}/${SNPTESTOUTPUTDATA}_RAW_${VARIANT}_excl_${EXCLUSION_TYPE}.sample -incl-range ${CHR}:${START}-${END}
echo "${QCTOOL2} -g ${GENETICDATA}/${SNPTESTDATA}${CHR}.bgen -s ${GENETICDATA}/${SNPTESTDATA}${CHR}.sample -excl-samples ${EXCLUSION_LIST} -og ${REGIONALDIR}/${SNPTESTOUTPUTDATA}_RAW_${VARIANT}_excl_${EXCLUSION_TYPE}.gen.gz -os ${REGIONALDIR}/${SNPTESTOUTPUTDATA}_RAW_${VARIANT}_excl_${EXCLUSION_TYPE}.sample -incl-range ${CHR}:${START}-${END} " > ${REGIONALDIR}/${STUDYNAME}_genex_${VARIANT}_excl_${EXCLUSION_TYPE}.sh
### ${QCTOOL} -g ${GENETICDATA}/${SNPTESTDATA}${CHR}.bgen -s ${GENETICDATA}/${SNPTESTDATA}${CHR}.sample -excl-samples ${EXCLUSION_LIST} -og ${REGIONALDIR}/${SNPTESTOUTPUTDATA}_RAW_${VARIANT}_excl_${EXCLUSION_TYPE}.gen.gz -os ${REGIONALDIR}/${SNPTESTOUTPUTDATA}_RAW_${VARIANT}_excl_${EXCLUSION_TYPE}.sample -incl-range ${CHR}:${START}-${END}
echo "${QCTOOL} -g ${GENETICDATA}/${SNPTESTDATA}${CHR}.bgen -s ${GENETICDATA}/${SNPTESTDATA}${CHR}.sample -excl-samples ${EXCLUSION_LIST} -og ${REGIONALDIR}/${SNPTESTOUTPUTDATA}_RAW_${VARIANT}_excl_${EXCLUSION_TYPE}.gen.gz -os ${REGIONALDIR}/${SNPTESTOUTPUTDATA}_RAW_${VARIANT}_excl_${EXCLUSION_TYPE}.sample -incl-range ${CHR}:${START}-${END} " > ${REGIONALDIR}/${STUDYNAME}_genex_${VARIANT}_excl_${EXCLUSION_TYPE}.sh
qsub -S /bin/bash -N GENEX${STUDYJOBNAME}_${VARIANT}_excl_${EXCLUSION_TYPE}_${PROJECTNAME} -e ${REGIONALDIR}/${STUDYNAME}_genex_${VARIANT}_excl_${EXCLUSION_TYPE}.errors -o ${REGIONALDIR}/${STUDYNAME}_genex_${VARIANT}_excl_${EXCLUSION_TYPE}.log -l h_rt=${QUEUE_QCTOOL} -l h_vmem=${VMEM_QCTOOL} -M ${EMAIL} -m ${MAILTYPE} -wd ${REGIONALDIR} ${REGIONALDIR}/${STUDYNAME}_genex_${VARIANT}_excl_${EXCLUSION_TYPE}.sh

elif [[ ${CHR} -eq "X" ]]; then
### FOR DEBUGGING
### ${QCTOOL2} -g ${GENETICDATA}/${SNPTESTDATA}${CHR}.bgen -s ${GENETICDATA}/${SNPTESTDATA}${CHR}.sample -excl-samples ${EXCLUSION_LIST} -og ${REGIONALDIR}/${SNPTESTOUTPUTDATA}_RAW_${VARIANT}_excl_${EXCLUSION_TYPE}.gen.gz -os ${REGIONALDIR}/${SNPTESTOUTPUTDATA}_RAW_${VARIANT}_excl_${EXCLUSION_TYPE}.sample -incl-range 0${CHR}:${START}-${END}
echo "${QCTOOL2} -g ${GENETICDATA}/${SNPTESTDATA}${CHR}.bgen -s ${GENETICDATA}/${SNPTESTDATA}${CHR}.sample -excl-samples ${EXCLUSION_LIST} -og ${REGIONALDIR}/${SNPTESTOUTPUTDATA}_RAW_${VARIANT}_excl_${EXCLUSION_TYPE}.gen.gz -os ${REGIONALDIR}/${SNPTESTOUTPUTDATA}_RAW_${VARIANT}_excl_${EXCLUSION_TYPE}.sample -incl-range 0${CHR}:${START}-${END} " > ${REGIONALDIR}/${STUDYNAME}_genex_${VARIANT}_excl_${EXCLUSION_TYPE}.sh
### ${QCTOOL} -g ${GENETICDATA}/${SNPTESTDATA}${CHR}.bgen -s ${GENETICDATA}/${SNPTESTDATA}${CHR}.sample -excl-samples ${EXCLUSION_LIST} -og ${REGIONALDIR}/${SNPTESTOUTPUTDATA}_RAW_${VARIANT}_excl_${EXCLUSION_TYPE}.gen.gz -os ${REGIONALDIR}/${SNPTESTOUTPUTDATA}_RAW_${VARIANT}_excl_${EXCLUSION_TYPE}.sample -incl-range 0${CHR}:${START}-${END}
echo "${QCTOOL} -g ${GENETICDATA}/${SNPTESTDATA}${CHR}.bgen -s ${GENETICDATA}/${SNPTESTDATA}${CHR}.sample -excl-samples ${EXCLUSION_LIST} -og ${REGIONALDIR}/${SNPTESTOUTPUTDATA}_RAW_${VARIANT}_excl_${EXCLUSION_TYPE}.gen.gz -os ${REGIONALDIR}/${SNPTESTOUTPUTDATA}_RAW_${VARIANT}_excl_${EXCLUSION_TYPE}.sample -incl-range 0${CHR}:${START}-${END} " > ${REGIONALDIR}/${STUDYNAME}_genex_${VARIANT}_excl_${EXCLUSION_TYPE}.sh
qsub -S /bin/bash -N GENEX${STUDYJOBNAME}_${VARIANT}_excl_${EXCLUSION_TYPE}_${PROJECTNAME} -e ${REGIONALDIR}/${STUDYNAME}_genex_${VARIANT}_excl_${EXCLUSION_TYPE}.errors -o ${REGIONALDIR}/${STUDYNAME}_genex_${VARIANT}_excl_${EXCLUSION_TYPE}.log -l h_rt=${QUEUE_QCTOOL} -l h_vmem=${VMEM_QCTOOL} -M ${EMAIL} -m ${MAILTYPE} -wd ${REGIONALDIR} ${REGIONALDIR}/${STUDYNAME}_genex_${VARIANT}_excl_${EXCLUSION_TYPE}.sh

else
Expand Down Expand Up @@ -807,13 +807,13 @@ else
### FOR DEBUGGING
### ${QTLTOOLKIT}/QTLPlotter.sh ${CONFIGURATIONFILE} ${SUMMARY} ${CLUMPDIR} ${CLUMP}
echo "${QTLTOOLKIT}/QTLPlotter.sh ${CONFIGURATIONFILE} ${SUMMARY} ${CLUMPDIR} ${CLUMP}"> ${SUMMARY}/${STUDYNAME}_QTLPlot_excl_${EXCLUSION_TYPE}.sh
qsub -S /bin/bash -N QTLPlot_${STUDYJOBNAME}_excl_${EXCLUSION_TYPE}_${PROJECTNAME} -hold_jid QTLParser_${STUDYJOBNAME}_excl_${EXCLUSION_TYPE}_${PROJECTNAME} -e ${SUMMARY}/${STUDYNAME}_QTLPlot_excl_${EXCLUSION_TYPE}.errors -o ${SUMMARY}/${STUDYNAME}_QTLPlot_excl_${EXCLUSION_TYPE}.log -l h_rt=04:00:00 -l h_vmem=16G -M ${EMAIL} -m ${MAILTYPE} -wd ${SUMMARY} ${SUMMARY}/${STUDYNAME}_QTLPlot_excl_${EXCLUSION_TYPE}.sh
qsub -S /bin/bash -N QTLPlot_${STUDYJOBNAME}_excl_${EXCLUSION_TYPE}_${PROJECTNAME} -hold_jid QTLParser_${STUDYJOBNAME}_excl_${EXCLUSION_TYPE}_${PROJECTNAME} -e ${SUMMARY}/${STUDYNAME}_QTLPlot_excl_${EXCLUSION_TYPE}.errors -o ${SUMMARY}/${STUDYNAME}_QTLPlot_excl_${EXCLUSION_TYPE}.log -l h_rt=${QUEUE_PLOT_CONFIG} -l h_vmem=${VMEM_PLOT_CONFIG} -M ${EMAIL} -m ${MAILTYPE} -wd ${SUMMARY} ${SUMMARY}/${STUDYNAME}_QTLPlot_excl_${EXCLUSION_TYPE}.sh
else

echo "* No clumping done - plotting regular QTL-analysis results. "
### ${QTLTOOLKIT}/QTLPlotter.sh ${CONFIGURATIONFILE} ${SUMMARY} ${CLUMPDIR} ${CLUMP}
echo "${QTLTOOLKIT}/QTLPlotter.sh ${CONFIGURATIONFILE} ${SUMMARY} ${CLUMPDIR} ${CLUMP}"> ${SUMMARY}/${STUDYNAME}_QTLPlot_excl_${EXCLUSION_TYPE}.sh
qsub -S /bin/bash -N QTLPlot_${STUDYJOBNAME}_excl_${EXCLUSION_TYPE}_${PROJECTNAME} -hold_jid QTLParser_${STUDYJOBNAME}_excl_${EXCLUSION_TYPE}_${PROJECTNAME} -e ${SUMMARY}/${STUDYNAME}_QTLPlot_excl_${EXCLUSION_TYPE}.errors -o ${SUMMARY}/${STUDYNAME}_QTLPlot_excl_${EXCLUSION_TYPE}.log -l h_rt=04:00:00 -l h_vmem=16G -M ${EMAIL} -m ${MAILTYPE} -wd ${SUMMARY} ${SUMMARY}/${STUDYNAME}_QTLPlot_excl_${EXCLUSION_TYPE}.sh
#### qsub -S /bin/bash -N QTLPlot_${STUDYJOBNAME}_excl_${EXCLUSION_TYPE}_${PROJECTNAME} -hold_jid QTLSum_${STUDYJOBNAME}_excl_${EXCLUSION_TYPE}_${PROJECTNAME} -e ${SUMMARY}/${STUDYNAME}_QTLPlot_excl_${EXCLUSION_TYPE}.errors -o ${SUMMARY}/${STUDYNAME}_QTLPlot_excl_${EXCLUSION_TYPE}.log -l h_rt=04:00:00 -l h_vmem=16G -M ${EMAIL} -m ${MAILTYPE} -wd ${SUMMARY} ${SUMMARY}/${STUDYNAME}_QTLPlot_excl_${EXCLUSION_TYPE}.sh
qsub -S /bin/bash -N QTLPlot_${STUDYJOBNAME}_excl_${EXCLUSION_TYPE}_${PROJECTNAME} -hold_jid QTLParser_${STUDYJOBNAME}_excl_${EXCLUSION_TYPE}_${PROJECTNAME} -e ${SUMMARY}/${STUDYNAME}_QTLPlot_excl_${EXCLUSION_TYPE}.errors -o ${SUMMARY}/${STUDYNAME}_QTLPlot_excl_${EXCLUSION_TYPE}.log -l h_rt=${QUEUE_PLOT_CONFIG} -l h_vmem=${VMEM_PLOT_CONFIG} -M ${EMAIL} -m ${MAILTYPE} -wd ${SUMMARY} ${SUMMARY}/${STUDYNAME}_QTLPlot_excl_${EXCLUSION_TYPE}.sh
fi

elif [[ ${ANALYSIS_TYPE} == "MQTL" ]]; then
Expand Down
7 changes: 2 additions & 5 deletions QTLChecker.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -105,8 +105,8 @@ echobold "+
echobold "+ +"
echobold "+ * Written by : Sander W. van der Laan +"
echobold "+ * E-mail : s.w.vanderlaan-2@umcutrecht.nl +"
echobold "+ * Last update : 2018-07-26 +"
echobold "+ * Version : 1.1.5 +"
echobold "+ * Last update : 2018-07-27 +"
echobold "+ * Version : 1.1.6 +"
echobold "+ +"
echobold "+ * Description : This script will check the regular nominal and permuted QTL results for success. +"
echobold "+ +"
Expand Down Expand Up @@ -145,9 +145,6 @@ else
### GENERIC SETTINGS
SOFTWARE=${SOFTWARE}
QTLTOOLKIT=${QTLTOOLKIT}
### FOR DEBUG
### QTLTOOLKIT=/hpc/dhl_ec/jschaap/QTLToolKit
### FOR DEBUG
QCTOOL=${QCTOOL}
SNPTEST252=${SNPTEST252}
QTLTOOLS=${QTLTOOLS}
Expand Down
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