qtl.config

### CONFIGURATION FILE FOR QTLTOOLKIT ###
# Precede your comments with a #-sign.
#
# Set the directory variables, the order doesn't matter.
# Don't end the directory variables with '/' (forward-slash)!
#
### --- SYSTEM SETTINGS --- ###
# REQUIRED: Path_to where the software resides on the server. 
SOFTWARE="/hpc/local/CentOS7/dhl_ec/software"
#
# REQUIRED: Path_to where QTLToolKit resides on the server.
QTLTOOLKIT=/hpc/dhl_ec/llandsmeer/_atheroexpress/_eqtl/QTLToolKit
#
#
# REQUIRED: Path_to support programs on the server
### Set location of SNPTEST v2.5.2 & the method to be used. 
### Note: QCTOOL v2.0 lacks the flags for filtering (-maf, -info, -hwe), so we extract
### in two steps - quick and dirty solution
SNPTEST=${SOFTWARE}/snptest_v2.5.2_CentOS6.5_x86_64_static/snptest_v2.5.2
QCTOOL=${SOFTWARE}/qctool_v1.5-linux-x86_64-static/qctool
QCTOOL2=${SOFTWARE}/qctool_v204
# QTLTOOLS=${SOFTWARE}/QTLTools/QTLtools_1.0_CentOS6.8_x86_64
QTLTOOLS=${SOFTWARE}/QTLtools_1.1_source/bin/QTLtools
QCTOOLKIT=${SOFTWARE}/QTLToolKit
LOCUSZOOM=${SOFTWARE}/locuszoom_1.3/bin/locuszoom
BGZIP=${SOFTWARE}/bgzip_v1.6
TABIX=${SOFTWARE}/tabix_v1.6
PLINK=${SOFTWARE}/plink_v1.9
PYTHON="/hpc/local/CentOS7/common/lang/python/2.7.10/bin/python"
#
### --- QSUB SETTINGS --- ###
QUEUE_QCTOOL_CONFIG="01:00:00"
VMEM_QCTOOL_CONFIG="8G"
QUEUE_NOM_CONFIG="08:00:00"
VMEM_NOM_CONFIG="8G"
QUEUE_PERM_CONFIG="32:00:00"
VMEM_PERM_CONFIG="8G"
QUEUE_CLUMP_CONFIG="00:30:00"
VMEM_CLUMP_CONFIG="12G"
QUEUE_SUMPARSER_CONFIG="00:15:00"
VMEM_SUMPARSER_CONFIG="8G"
QUEUE_FUNCENRICH_CONFIG="12:00:00"
VMEM_FUNCENRICH_CONFIG="64G"
QUEUE_RTC_CONFIG="00:30:00"
VMEM_RTC_CONFIG="12G"
QUEUE_PLOT_CONFIG="24:00:00"
VMEM_PLOT_CONFIG="16G"
#
### --- ANALYSIS SETTINGS --- ###
# REQUIRED: mailing settings
# you're e-mail address; you'll get an email when the job has ended or when it was aborted
# 'b' Mail is sent at the beginning of the job; 
# 'e' Mail is sent at the end of the job; 
# 'a' Mail is sent when the job is aborted or rescheduled.
# 's' Mail is sent when the job is suspended;
# 'n' No mail is sent.
YOUREMAIL="atheroexpress@sink.qstatbot.com"
MAILSETTINGS="beas" 
#
# REQUIRED: Path_to where the main alysis directory resides.
ROOTDIR=/hpc/dhl_ec/llandsmeer/_atheroexpress/_eqtl/_rootdir

#
# REQUIRED: Name of the project.
# PROJECTNAME="cardiogramplusc4d_57loci_4real_complete_with_4pcs_clumped"
# PROJECTNAME="cardiogramplusc4d_88loci_4real_complete_with_4pcs_clumped"
PROJECTNAME="2020-03-03_test_slurm-v3"
# PROJECTNAME="cardiogramplusc4d_small_4real_complete_with_4pcs"
# PROJECTNAME="cardiogramplusc4d_TEST_4real_complete_with_4pcs"
#
# REQUIRED: Analysis settings.
# You can choose one of these options [CIS/TRANS].
QTL_TYPE="CIS"
#
# REQUIRED: Set study and sample type
# Set the analysis type, choose one of these options [AEMS450K1/AEMS450K2/CTMM]
STUDY_TYPE="AERNA" 
#
# Set the sample type, choose one of these options [AE: PLAQUES/BLOOD; CTMM: MONOCYTES]
SAMPLE_TYPE="BLOOD"
#
# Set the analysis type, choose one of these options [AE: MQTL; CTMM: EQTL]
ANALYSIS_TYPE="EQTL"
#
# REQUIRED: Set the regions to analyse 
REGIONS_FILE="/hpc/dhl_ec/llandsmeer/ae/fifth_try/variants_for_eqtl.10loci.txt"
#
# REQUIRED: Set the exclusion type and the list of covariates *not* to use in the model
EXCLUSION_COV="${ROOTDIR}/excl_cov.txt"
EXCLUSION_COV="/hpc/dhl_ec/llandsmeer/_atheroexpress/_eqtl/_data/excl_cov"
#
# REQRUIRED: Set STUDY-specific directories and files
#
# Choose a name for file names, options: [aegs/ctmm]
STUDYNAME="aegs"
# Choose the study job-name, options: [AEMS450K1/AEMS450K2/CTMM]
STUDYJOBNAME="AERNA"
#
# Choose the matching genotyping and expression/methylation data
#
### -- my config ###
ORIGINALS="/hpc/dhl_ec/data/_ae_originals"
GENETICDATA=/hpc/dhl_ec/llandsmeer/_atheroexpress/_eqtl/_data/AEGS_COMBINED_QC2018
SNPTESTDATA="AEGS1_2_3.clean.v5.chr"
SNPTESTOUTPUTDATA="aegs_combined"
PHENOCOVEXCL="${ORIGINALS}/pheno_cov_exclusions"

OMICSDATA=/hpc/dhl_ec/llandsmeer/_atheroexpress/_eqtl/_data
QTLDATA=${OMICSDATA}/counts.qc.bed.gz
QTLINDEX=${OMICSDATA}/counts.gc.bed.gz.tbi
### --- ATHERO-EXPRESS --- ###
# #
# ORIGINALS="/hpc/dhl_ec/data/_ae_originals"
# GENETICDATA="${ORIGINALS}/AEGS_COMBINED_IMPUTE2_1000Gp3_GoNL5"
# OMICSDATA="${ORIGINALS}/${STUDYJOBNAME}"
# SNPTESTDATA="aegs_combo_1kGp3GoNL5_RAW_chr"
# SNPTESTOUTPUTDATA="aegs_1kGp3GoNL5"
# # for PLAQUES analysis
# # AEMS450K1
# QTLDATA="${OMICSDATA}/20170924.AEMS450K1.BvaluesQCplaque.bed.gz"
# QTLINDEX="${OMICSDATA}/20170924.AEMS450K1.BvaluesQCplaque.bed.gz.tbi"
# # AEMS450K2
# QTLDATA="${OMICSDATA}/20170924.AEMS450K2.BvaluesQCplaque.bed.gz"
# QTLINDEX="${OMICSDATA}/20170924.AEMS450K2.BvaluesQCplaque.bed.gz.tbi"
# # for BLOOD analysis
# # AEMS450K1
# QTLDATA="${OMICSDATA}/20170924.AEMS450K1.BvaluesQCblood.bed.gz"
# QTLINDEX="${OMICSDATA}/20170924.AEMS450K1.BvaluesQCblood.bed.gz.tbi"
# # AEMS450K2
# # There is no data for AEMS450K2
# #
# # Indicate the COVARIATE-data to use
# COVARIATES="${GENETICDATA}/covariates_aegs_combo.all.cov"
# #
# # Indicate the ANNOTATION-file to use
# ANNOTATIONFILE="${ORIGINALS}/IlluminaMethylation450K.annotation.txt.gz"
#
### --- CTMM --- ### 
# ORIGINALS="/hpc/dhl_ec/data/_ctmm_originals"
# GENETICDATA="${ORIGINALS}/CTMMAxiomTX_IMPUTE2_1000Gp3_GoNL5"
# PHENOCOVEXCL="${ORIGINALS}/pheno_cov_exclusions"
# OMICSDATA="${ORIGINALS}/CTMMHumanHT12v4r2_15002873B"
# SNPTESTDATA="ctmm_1kGp3GoNL5_RAW_chr"
# SNPTESTOUTPUTDATA="ctmm_1kGp3GoNL5"
# QTLDATA="${OMICSDATA}/ctmm.humanhtv4r2.qtl.bed.gz"
# QTLINDEX="${OMICSDATA}/ctmm.humanhtv4r2.qtl.bed.gz.tbi"
#
# Indicate the COVARIATE-data to use
COVARIATES="${PHENOCOVEXCL}/covariates_aegs_combo.all.cov"
COVARIATES="/hpc/dhl_ec/llandsmeer/_atheroexpress/_eqtl/_data/COVARIATES"
#
# Indicate the ANNOTATION-file to use
ANNOTATIONFILE="/hpc/dhl_ec/llandsmeer/_atheroexpress/_eqtl/_data/ANNOTATION"

#
### --- EXCLUSION TYPE & LIST--- ###
### Note: All analyses with ATHERO-EXPRESS data are presumed to be constrained to CEA-patients only.
###       You can set the exclusion criteria 'NONAEGS/FEMALES/MALES' if you want to analyse
###       all ATHERO-EXPRESS data!
# Set the exclusion type.
# For the ATHERO-EXPRESS, choose one of these options [DEFAULT/SMOKER/NONSMOKER/MALES/FEMALES/T2D/NONT2D/CKD/NONCKD/PRE2007/POST2007/NONAEGS/NONAEGSFEMALES/NONAEGSMALES]
# For the CTMM, choose one of these options [DEFAULT/SMOKER/NONSMOKER/MALES/FEMALES/T2D/NONT2D]
#
# ### ATHERO-EXPRESS specific exclusion lists
# EXCLUSION_TYPE="DEFAULT" 
# EXCLUSION_LIST="${GENETICDATA}/exclusion_nonCEA.list"
# ### MALES ONLY ANALYSIS
# EXCLUSION_TYPE="EXCL_FEMALES"
# EXCLUSION_LIST="${GENETICDATA}/exclusion_nonCEA_Females.list"
# ### FEMALES ONLY ANALYSIS
# EXCLUSION_TYPE="EXCL_MALES"
# EXCLUSION_LIST="${GENETICDATA}/exclusion_nonCEA_Males.list"
# ### NON-CKD ONLY ANALYSIS
# EXCLUSION_TYPE="EXCL_CKD"
# EXCLUSION_LIST="${GENETICDATA}/exclusion_nonCEA_CKD.list"
# ### CKD ONLY ANALYSIS
# EXCLUSION_TYPE="EXCL_NONCKD"
# EXCLUSION_LIST="${GENETICDATA}/exclusion_nonCEA_nonCKD.list"
# ### NON-TYPE 2 DIABETES ONLY ANALYSIS
# EXCLUSION_TYPE="EXCL_T2D"
# EXCLUSION_LIST="${GENETICDATA}/exclusion_nonCEA_T2D.list"
# ### TYPE 2 DIABETES ONLY ANALYSIS
# EXCLUSION_TYPE="EXCL_NONT2D"
# EXCLUSION_LIST="${GENETICDATA}/exclusion_nonCEA_nonT2D.list"
# ### SMOKER ONLY ANALYSIS
# EXCLUSION_TYPE="EXCL_SMOKER"
# EXCLUSION_LIST="${GENETICDATA}/exclusion_nonCEA_nonSMOKER.list"
# ### NONSMOKER ONLY ANALYSIS
# EXCLUSION_TYPE="EXCL_NONSMOKER"
# EXCLUSION_LIST="${GENETICDATA}/exclusion_nonCEA_SMOKER.list"
# ### POST-2007 ONLY ANALYSIS
# EXCLUSION_TYPE="EXCL_PRE2007"
# EXCLUSION_LIST="${GENETICDATA}/exclusion_nonCEA_pre2007.list"
# ### PRE-2007 ONLY ANALYSIS
# EXCLUSION_TYPE="EXCL_POST2007"
# EXCLUSION_LIST="${GENETICDATA}/exclusion_nonCEA_post2007.list"
# ### NON-DIURETICS ONLY ANALYSIS
# EXCLUSION_TYPE="EXCL_DIURETICS"
# EXCLUSION_LIST="${GENETICDATA}/exclusion_nonCEA_DIURETICS.list"
# ### DIURETICS ONLY ANALYSIS
# EXCLUSION_TYPE="EXCL_NONDIURETICS"
# EXCLUSION_LIST="${GENETICDATA}/exclusion_nonCEA_nonDIURETICS.list"
#
### CTMMGS specific exclusion lists
EXCLUSION_TYPE="EXCL_DEFAULT"
EXCLUSION_LIST="${PHENOCOVEXCL}/exclusion_nonCTMM.list"
EXCLUSION_LIST="${PHENOCOVEXCL}/exclusion_nonAEGS.list"
EXCLUSION_LIST="/hpc/dhl_ec/llandsmeer/ae/fifth_try/phenocov_excl/exclusion_nonAEGS.list"
# ### MALES ONLY ANALYSIS
# EXCLUSION_TYPE="EXCL_FEMALES"
# EXCLUSION_LIST="${PHENOCOVEXCL}/exclusion_nonCTMM_FEMALES.list"
# ### FEMALES ONLY ANALYSIS
# EXCLUSION_TYPE="EXCL_MALES"
# EXCLUSION_LIST="${PHENOCOVEXCL}/exclusion_nonCTMM_MALES.list"
# ### NON-CKD ONLY ANALYSIS
# EXCLUSION_TYPE="EXCL_CKD" #-- does not exist yet
# EXCLUSION_LIST="${PHENOCOVEXCL}/exclusion_nonCTMM_CKD.list"
# ### CKD ONLY ANALYSIS
# EXCLUSION_TYPE="EXCL_NONCKD" #-- does not exist yet
# EXCLUSION_LIST="${PHENOCOVEXCL}/exclusion_nonCTMM_nonCKD.list"
# ### NON-TYPE 2 DIABETES ONLY ANALYSIS
# EXCLUSION_TYPE="EXCL_T2D"
# EXCLUSION_LIST="${PHENOCOVEXCL}/exclusion_nonCTMM_T2D.list"
# ### TYPE 2 DIABETES ONLY ANALYSIS
# EXCLUSION_TYPE="EXCL_NONT2D"
# EXCLUSION_LIST="${PHENOCOVEXCL}/exclusion_nonCTMM_nonT2D.list"
# ### SMOKER ONLY ANALYSIS
# EXCLUSION_TYPE="EXCL_SMOKER"
# EXCLUSION_LIST="${PHENOCOVEXCL}/exclusion_nonCTMM_SMOKER.list"
# ### NONSMOKER ONLY ANALYSIS
# EXCLUSION_TYPE="EXCL_NONSMOKER"
# EXCLUSION_LIST="${PHENOCOVEXCL}/exclusion_nonCTMM_nonSMOKER.list"
# ### NON-DIURETICS ONLY ANALYSIS
# EXCLUSION_TYPE="EXCL_DIURETICS"
# EXCLUSION_LIST="${PHENOCOVEXCL}/exclusion_nonCTMM_DIURETICS.list"
# ### DIURETICS ONLY ANALYSIS
# EXCLUSION_TYPE="EXCL_NONDIURETICS"
# EXCLUSION_LIST="${PHENOCOVEXCL}/exclusion_nonCTMM_nonDIURETICS.list"
# ### ANALYSIS IN DATA WITH MONOCYTE COUNTS
# EXCLUSION_TYPE="EXCL_NONMONOCYTE"
# EXCLUSION_LIST="${PHENOCOVEXCL}/exclusion_nonCTMM_nonMONOCYTE.list"

### --- QTL SETTINGS --- ###
SEEDNO_CONFIG=91149216
PERMSTART_CONFIG="1000"
PERMEND_CONFIG="10000"
NOMINAL_P="0.05"

### --- QCTOOL SETTINGS --- ###
MAF_CONFIG="0.05"
INFO_CONFIG="0.8"
HWE_CONFIG="6"

### --- CLUMPING SETTINGS --- ###
CLUMP="Y" # plot clumped set? [Y/N]
CLUMP_THRESH="0.8" # Threshold for rsquared, optional
# CLUMP_GWAS="${ROOTDIR}/cardiogramplusc4d.cad.57loci.forclumping.txt"
CLUMP_GWAS="${ROOTDIR}/cardiogramplusc4d.cad.88loci.forclumping.txt"
CLUMP_GWAS="/hpc/dhl_ec/llandsmeer/_atheroexpress/_eqtl/_data/cardiogramplusc4d.cad.164loci.forclumping.txt"
CLUMP_P1="5e-8"
CLUMP_P2="0.05"
CLUMP_KB="1000"
CLUMP_GWAS_SNPFIELD="SNP"
CLUMP_GWAS_PVAL="P"

### --- LOCUSZOOM SETTINGS --- ###
# REGASSOCPLOT            -- Do you want to plot regional associations using LocusZoom v1.3? default: N
# LDPOP                   -- Indicates the reference population for the LD map used by LocusZoom v1.3. default: EUR.
# LDBUILD                 -- Indicates the genome build used by LocusZoom v1.3. default: hg19.
# LDSOURCE                -- Indicates the reference source used by LocusZoom v1.3. default: 1000G_March2012.
# LDSETTINGS              -- Fill in specifica settings to be used by LocusZoom v1.3. 
# LZMARKERNAME            -- Column name containing the variants used in the input data for LocusZoom v1.3. default: MarkerName.
# LZPVALUE                -- Column name containing the p-values used in the input data for LocusZoom v1.3. default: P-value.
# LZDELIMITER             -- Delimiter for the input data used by LocusZoom v1.3. default: tab.
# LZTHEME                 -- Theme used by LocusZoom v1.3 for plotting. default: publication
REGASSOCPLOT="Y"
LDPOP="EUR"
LDBUILD="hg19"
LDSOURCE="1000G_March2012"
LOCUSZOOM_SETTINGS="ldColors=\"#595A5C,#4C81BF,#1396D8,#C5D220,#F59D10,red,#9A3480\" showRecomb=TRUE drawMarkerNames=FALSE showRug=FALSE showAnnot=TRUE showRefsnpAnnot=TRUE showGenes=TRUE clean=TRUE bigDiamond=TRUE rfrows=10 refsnpLineWidth=2 refsnpTextSize=1.0 axisSize=1.25 axisTextSize=1.25 geneFontSize=1.25"
LZMARKERNAME="MarkerName"
LZPVALUE="P-value"
LZDELIMITER="tab"
LZTHEME="publication"

### --- RTC SETTINGS --- ###
# RTCCALCULATION		-- Calculate RTC score? [Y/N]
# RTCTYPE				-- When doing a genome-wide QTL analysis choose 'NORMAL', if using a selection of independent variants 'CONDITIONAL'
# RTCPVALLEVEL			-- QTL p-value threshold to select variants for input to RTC analysis
# RTCGWAS				-- Variants annotated to GWAS loci, two main versions: 
#							* 'GWAS.b37.1kGp3GoNL5.txt' includes rsID-based variant names, specifically for 1000G phase 3 + GoNL5 imputed data.
#							* 'GWAS.b37.txt' includes chr_bp variant names
#                           * 'GWAS.b37.1kGp3GoNL5.handcurated_20180725.txt' includes rsID-based variant names (1kGp3 + GoNL5) and hand-curated from GWAS Catalog on 2018-07-25
# RTCHOTSPOTS			-- File containing genome-wide (b37) hotspots

### --- FUNCTIONAL ENRICHMENT SETTINGS --- ###
# FUNCENRICH			-- Perform functional enrichment?
# FUNCINFORMATION		-- Some file with functional information, e.g. genome-wide transcription binding factors. There are two files available:
#                           * 'TFs.encode.sort.withzero.bed': with two digit chromosomes
#                           * 'TFs.encode.sort.bed': one or two digit chromosomes.
#                           * 'H3K27ac.encode.monocytescd14pos.bed': with two digit chromosomes; epigentic marker of actively enhanced in monocytes CD14+
#                           * 'H3K4me1.encode.monocytescd14pos.bed': with two digit chromosomes; epigentic marker of transcription in monocytes CD14+
#                           * 'H3K4me3.encode.monocytescd14pos.bed': with two digit chromosomes; epigentic marker in monocytes CD14+
#                           * 'DNAse.encode.monocytescd14pos.bed': with two digit chromosomes; open chromatin markers in monocytes CD14+
#                           * 'H3K27ac.DNAse.active.encode.monocytescd14pos.bed': with two digit chromosomes; open chromatin markers intersected with actively enhanced H3K27ac markers in monocytes CD14+
# FUNCINFOFILENAME      -- This will be printed as part of the functional enrichment analysis output-filename.
RTCCALCULATION="Y"
RTCTYPE="CONDITIONAL"
RTCPVALLEVEL="0.05"
RTCGWAS="GWAS.b37.1kGp3GoNL5.handcurated_20180725.txt"
RTCHOTSPOTS="hotspots_b37_hg19.bed"
FUNCENRICH="Y"
FUNCINFORMATION="H3K27ac.encode.monocytescd14pos.bed"
FUNCINFOFILENAME="H3K27ac.encode.monocytescd14pos"
# FUNCINFORMATION="H3K4me1.encode.monocytescd14pos.bed"
# FUNCINFOFILENAME="H3K4me1.encode.monocytescd14pos"
# FUNCINFORMATION="H3K4me3.encode.monocytescd14pos.bed"
# FUNCINFOFILENAME="H3K4me3.encode.monocytescd14pos"
# FUNCINFORMATION="DNAse.encode.monocytescd14pos.bed"
# FUNCINFOFILENAME="DNAse.encode.monocytescd14pos"
# FUNCINFORMATION="H3K27ac.DNAse.active.encode.monocytescd14pos.bed"
# FUNCINFOFILENAME="H3K27ac.DNAse.active.encode.monocytescd14pos"