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@@ -124,11 +124,10 @@ echobold "+ | |
| echobold "+ +" | ||
| echobold "+ * Written by : Sander W. van der Laan +" | ||
| echobold "+ * E-mail : [email protected] +" | ||
| echobold "+ * Last update : 2017-03-10 +" | ||
| echobold "+ * Version : 2.1.0 +" | ||
| echobold "+ * Last update : 2017-09-19 +" | ||
| echobold "+ * Version : 2.2.0 +" | ||
| echobold "+ +" | ||
| echobold "+ * Description : This script will set some directories, execute something in a for-loop, and will then +" | ||
| echobold "+ submit this in a job. +" | ||
| echobold "+ * Description : This script will set some directories and variables, and than run a QTL analysis. +" | ||
| echobold "+ +" | ||
| echobold "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++" | ||
| echo "Today's date and time: "$(date) | ||
|
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@@ -211,7 +210,7 @@ else | |
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| ### SOURCE THE CONFIGURATION FILE | ||
| source ${11} | ||
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| ### QSUB SETTINGS | ||
| ### --- THESE COULD BE ARGUMENTS --- ### | ||
| QUEUE_QCTOOL=${QUEUE_QCTOOL_CONFIG} | ||
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@@ -239,7 +238,7 @@ else | |
| ### AEMS450K1 SPECIFIC -- DO NOT CHANGE | ||
| ORIGINALS=/hpc/dhl_ec/data/_ae_originals | ||
| GENETICDATA=${ORIGINALS}/AEGS_COMBINED_IMPUTE2_1000Gp3_GoNL5 | ||
| AEMS450K1=${ORIGINALS}/AEMethylS_IlluminaMethylation450K | ||
| AEMS450K1=${ORIGINALS}/AEMS450K1 | ||
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| ### for file names | ||
| STUDYNAME="aegs" | ||
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@@ -248,11 +247,11 @@ else | |
| #SNPTESTSAMPLEDATA="" | ||
| SNPTESTOUTPUTDATA="aegs_1kGp3GoNL5" | ||
| if [[ ${SAMPLE_TYPE} == "PLAQUES" ]]; then | ||
| FASTQTLDATA="${AEMS450K1}/AEM_mQTL_INPUT_DATA/aems450k1_QC_443872_plaques.bed.gz" | ||
| FASTQTLINDEX="${AEMS450K1}/AEM_mQTL_INPUT_DATA/aems450k1_QC_443872_plaques.bed.gz.tbi" | ||
| FASTQTLDATA="${AEMS450K1}/450k1_Mvalues_plaque.fastQTL.sorted.bed.gz" | ||
| FASTQTLINDEX="${AEMS450K1}/450k1_Mvalues_plaque.fastQTL.sorted.bed.gz.tbi" | ||
| elif [[ ${STUDY_TYPE} == "BLOOD" ]]; then | ||
| FASTQTLDATA="${AEMS450K1}/AEM_mQTL_INPUT_DATA/aems450k1_QC_443872_blood.bed.gz" | ||
| FASTQTLINDEX="${AEMS450K1}/AEM_mQTL_INPUT_DATA/aems450k1_QC_443872_blood.bed.gz.tbi" | ||
| FASTQTLDATA="${AEMS450K1}/450k1_Mvalues_blood.fastQTL.sorted.bed.gz" | ||
| FASTQTLINDEX="${AEMS450K1}/450k1_Mvalues_blood.fastQTL.sorted.bed.gz.tbi" | ||
| else | ||
| echo " *** ERROR *** " | ||
| echo "Something is rotten in the City of Gotham; most likely a typo. " | ||
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@@ -276,11 +275,8 @@ else | |
| #SNPTESTSAMPLEDATA="" | ||
| SNPTESTOUTPUTDATA="aegs_1kGp3GoNL5" | ||
| if [[ ${SAMPLE_TYPE} == "PLAQUES" ]]; then | ||
| FASTQTLDATA="${AEMS450K2}/AEM_mQTL_INPUT_DATA/aems450k2_QC_443872_plaques.bed.gz" | ||
| FASTQTLINDEX="${AEMS450K2}/AEM_mQTL_INPUT_DATA/aems450k2_QC_443872_plaques.bed.gz.tbi" | ||
| elif [[ ${STUDY_TYPE} == "BLOOD" ]]; then | ||
| FASTQTLDATA="${AEMS450K2}/AEM_mQTL_INPUT_DATA/aems450k2_QC_443872_blood.bed.gz" | ||
| FASTQTLINDEX="${AEMS450K2}/AEM_mQTL_INPUT_DATA/aems450k2_QC_443872_blood.bed.gz.tbi" | ||
| FASTQTLDATA="${AEMS450K2}/450k2_Mvalues_plaque.fastQTL.sorted.bed.gz" | ||
| FASTQTLINDEX="${AEMS450K2}/450k2_Mvalues_plaque.fastQTL.sorted.bed.gz.tbi" | ||
| else | ||
| echo " *** ERROR *** " | ||
| echo "Something is rotten in the City of Gotham; most likely a typo. " | ||
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