From c3d361756fa64d8ec6e64ef95a06b4bf0db8330e Mon Sep 17 00:00:00 2001 From: swvanderlaan Date: Thu, 24 Aug 2017 23:55:28 +0200 Subject: [PATCH] Edits to the configuration file to accomodate new conditional analysis function --- gwastoolkit.conf | 62 ++++++++++++++++++++++-------------------------- 1 file changed, 29 insertions(+), 33 deletions(-) diff --git a/gwastoolkit.conf b/gwastoolkit.conf index 9ca8053..10ba12e 100755 --- a/gwastoolkit.conf +++ b/gwastoolkit.conf @@ -65,16 +65,16 @@ MAILSETTINGS="a" # # ANALYSIS SETTINGS # REQUIRED: Path_to where the main alysis directory resides. -PROJECTDIR="/hpc/dhl_ec/svanderlaan/projects/lookups/cyp2c19" +PROJECTDIR="/hpc/dhl_ec/svanderlaan/projects/lookups/furin_fes_shuye_samani" # # REQUIRED: Name of the project. -PROJECTNAME="CYP2C19" +PROJECTNAME="FURIN_FES_CONDITIONAL_on_rs17514846" # # REQUIRED: Analysis settings. # You can choose one of these options [GWAS/VARIANT/REGION/GENES]. ANALYSIS_TYPE="VARIANT" # You can choose one of these options [AEGS/AAAGS/CTMM]. -STUDY_TYPE="CTMM" +STUDY_TYPE="AEGS" # # REQUIRED: give a list of covariates in a file # Example covariate-list format: @@ -87,7 +87,7 @@ PHENOTYPE_FILE="${PROJECTDIR}/phenotypes.txt" # SPECIFIC DATA SETTINGS # REQUIRED: location of [imputed] data to use -- all BGEN-format. # ### AEGS, 1000G phase 3, GoNL5 -# IMPUTEDDATA="/hpc/dhl_ec/data/_ae_originals/AEGS_COMBINED_IMPUTE2_1000Gp3_GoNL5/aegs_combo_1kGp3GoNL5_RAW_chr" +IMPUTEDDATA="/hpc/dhl_ec/data/_ae_originals/AEGS_COMBINED_IMPUTE2_1000Gp3_GoNL5/aegs_combo_1kGp3GoNL5_RAW_chr" # ### AEGS, 1000G phase 1 # IMPUTEDDATA="/hpc/dhl_ec/data/_ae_originals/AEGS_COMBINED_IMPUTE2_BBMRI_1000Gp1v3/aegs_combo_1000g_RAW_chr" # ### AEGS, GoNL4 @@ -95,25 +95,25 @@ PHENOTYPE_FILE="${PROJECTDIR}/phenotypes.txt" ### AAAGS, 1000G phase 3, GoNL5 # IMPUTEDDATA="/hpc/dhl_ec/data/_aaa_originals/AAAGS_IMPUTE2_1000Gp3_GoNL5/aaags_1kGp3GoNL5_RAW_chr" # ### CTMMGS, 1000G phase 3, GoNL5 -IMPUTEDDATA="/hpc/dhl_ec/data/_ctmm_originals/CTMMAxiomTX_IMPUTE2_1000Gp3_GoNL5/ctmm_1kGp3GoNL5_RAW_chr" +# IMPUTEDDATA="/hpc/dhl_ec/data/_ctmm_originals/CTMMAxiomTX_IMPUTE2_1000Gp3_GoNL5/ctmm_1kGp3GoNL5_RAW_chr" # # REQUIRED: location of sample file. ### Set the phenotype file: # ### AEGS -# SAMPLE_FILE="/hpc/dhl_ec/data/_ae_originals/AEGS_COMBINED_IMPUTE2_1000Gp3_GoNL5/aegscombo_phenocov.sample" +SAMPLE_FILE="/hpc/dhl_ec/data/_ae_originals/AEGS_COMBINED_IMPUTE2_1000Gp3_GoNL5/aegscombo_phenocov.sample" # ### AAAGS # SAMPLE_FILE="/hpc/dhl_ec/data/_aaa_originals/AAAGS_IMPUTE2_1000Gp3_GoNL5/aaags_phenocov.sample" # ### CTMMGS -SAMPLE_FILE="/hpc/dhl_ec/data/_ctmm_originals/CTMMAxiomTX_IMPUTE2_1000Gp3_GoNL5/ctmm_phenocov.sample" +# SAMPLE_FILE="/hpc/dhl_ec/data/_ctmm_originals/CTMMAxiomTX_IMPUTE2_1000Gp3_GoNL5/ctmm_phenocov.sample" # # REQUIRED: exclusion-lists ### SampleID123X ### SampleID123Y ### SampleID123Z - +# # ### AEGS specific exclusion lists -# EXCLUSION="EXCL_DEFAULT" -# EXCLUSION_LIST=/hpc/dhl_ec/data/_ae_originals/AEGS_COMBINED_IMPUTE2_1000Gp3_GoNL5/exclusion_nonCEA.list +EXCLUSION="EXCL_DEFAULT" +EXCLUSION_LIST=/hpc/dhl_ec/data/_ae_originals/AEGS_COMBINED_IMPUTE2_1000Gp3_GoNL5/exclusion_nonCEA.list # EXCLUSION="EXCL_FEMALES" # EXCLUSION_LIST=/hpc/dhl_ec/data/_ae_originals/AEGS_COMBINED_IMPUTE2_1000Gp3_GoNL5/exclusion_nonCEA_Females.list # EXCLUSION="EXCL_MALES" @@ -166,37 +166,28 @@ SAMPLE_FILE="/hpc/dhl_ec/data/_ctmm_originals/CTMMAxiomTX_IMPUTE2_1000Gp3_GoNL5/ # EXCLUSION_LIST="/hpc/dhl_ec/data/_aaa_originals/AAAGS_IMPUTE2_1000Gp3_GoNL5/exclusion_nonAAAGSnonAAA.list" ### CTMMGS specific exclusion lists -EXCLUSION="EXCL_DEFAULT" -EXCLUSION_LIST="/hpc/dhl_ec/data/_ctmm_originals/CTMMAxiomTX_IMPUTE2_1000Gp3_GoNL5/exclusion_nonCTMM.list" -# EXCLUSION="EXCL_FEMALES" +# ### EXCLUSION="EXCL_DEFAULT" +# EXCLUSION_LIST="/hpc/dhl_ec/data/_ctmm_originals/CTMMAxiomTX_IMPUTE2_1000Gp3_GoNL5/exclusion_nonCTMM.list" +# ### EXCLUSION="EXCL_FEMALES" # EXCLUSION_LIST="/hpc/dhl_ec/data/_ctmm_originals/CTMMAxiomTX_IMPUTE2_1000Gp3_GoNL5/exclusion_nonCTMM_FEMALES.list" -# EXCLUSION="EXCL_MALES" +# ### EXCLUSION="EXCL_MALES" # EXCLUSION_LIST="/hpc/dhl_ec/data/_ctmm_originals/CTMMAxiomTX_IMPUTE2_1000Gp3_GoNL5/exclusion_nonCTMM_MALES.list" -# EXCLUSION="EXCL_CKD" -- does not exist yet -# EXCLUSION_LIST="/hpc/dhl_ec/data/_ctmm_originals/CTMMAxiomTX_IMPUTE2_1000Gp3_GoNL5/exclusion_nonCTMM_CKD.list" -# EXCLUSION="EXCL_NONCKD" -- does not exist yet -# EXCLUSION_LIST="/hpc/dhl_ec/data/_ctmm_originals/CTMMAxiomTX_IMPUTE2_1000Gp3_GoNL5/exclusion_nonCTMM_nonCKD.list" -# EXCLUSION="EXCL_T2D" +# ### EXCLUSION="EXCL_CKD" -- does not exist yet +# ###EXCLUSION_LIST="/hpc/dhl_ec/data/_ctmm_originals/CTMMAxiomTX_IMPUTE2_1000Gp3_GoNL5/exclusion_nonCTMM_CKD.list" +# ### EXCLUSION="EXCL_NONCKD" -- does not exist yet +# ###EXCLUSION_LIST="/hpc/dhl_ec/data/_ctmm_originals/CTMMAxiomTX_IMPUTE2_1000Gp3_GoNL5/exclusion_nonCTMM_nonCKD.list" +# ### EXCLUSION="EXCL_T2D" # EXCLUSION_LIST="/hpc/dhl_ec/data/_ctmm_originals/CTMMAxiomTX_IMPUTE2_1000Gp3_GoNL5/exclusion_nonCTMM_T2D.list" -# EXCLUSION="EXCL_NONT2D" +# ### EXCLUSION="EXCL_NONT2D" # EXCLUSION_LIST="/hpc/dhl_ec/data/_ctmm_originals/CTMMAxiomTX_IMPUTE2_1000Gp3_GoNL5/exclusion_nonCTMM_nonT2D.list" -# EXCLUSION="EXCL_SMOKER" +# ### EXCLUSION="EXCL_SMOKER" # EXCLUSION_LIST="/hpc/dhl_ec/data/_ctmm_originals/CTMMAxiomTX_IMPUTE2_1000Gp3_GoNL5/exclusion_nonCTMM_SMOKER.list" -# EXCLUSION="EXCL_NONSMOKER" +# ### EXCLUSION="EXCL_NONSMOKER" # EXCLUSION_LIST="/hpc/dhl_ec/data/_ctmm_originals/CTMMAxiomTX_IMPUTE2_1000Gp3_GoNL5/exclusion_nonCTMM_nonSMOKER.list" # EXCLUSION="EXCL_DIURETICS" # EXCLUSION_LIST="/hpc/dhl_ec/data/_ctmm_originals/CTMMAxiomTX_IMPUTE2_1000Gp3_GoNL5/exclusion_nonCTMM_DIURETICS.list" # EXCLUSION="EXCL_NONDIURETICS" # EXCLUSION_LIST="/hpc/dhl_ec/data/_ctmm_originals/CTMMAxiomTX_IMPUTE2_1000Gp3_GoNL5/exclusion_nonCTMM_nonDIURETICS.list" -# EXCLUSION="EXCL_CLOPIDOGREL" -# EXCLUSION_LIST="/hpc/dhl_ec/data/_ctmm_originals/CTMMAxiomTX_IMPUTE2_1000Gp3_GoNL5/exclusion_nonCTMM_CLOPIDOGREL.list" -# EXCLUSION="EXCL_NONCLOPIDOGREL" -# EXCLUSION_LIST="/hpc/dhl_ec/data/_ctmm_originals/CTMMAxiomTX_IMPUTE2_1000Gp3_GoNL5/exclusion_nonCTMM_nonCLOPIDOGREL.list" -# EXCLUSION="EXCL_NONLEIDEN" -# EXCLUSION_LIST="/hpc/dhl_ec/data/_ctmm_originals/CTMMAxiomTX_IMPUTE2_1000Gp3_GoNL5/exclusion_nonCTMM_nonLEIDEN.list" -# EXCLUSION="EXCL_NONLEIDENONLYCLOPIDOGREL" -# EXCLUSION_LIST="/hpc/dhl_ec/data/_ctmm_originals/CTMMAxiomTX_IMPUTE2_1000Gp3_GoNL5/exclusion_nonCTMM_nonLEIDENonlyCLOPIDOGREL.list" - # REQUIRED: ANALYSIS SPECIFIC ARGUMENTS # For per-variant analysis @@ -208,9 +199,14 @@ EXCLUSION_LIST="/hpc/dhl_ec/data/_ctmm_originals/CTMMAxiomTX_IMPUTE2_1000Gp3_GoN VARIANTLIST="${PROJECTDIR}/variantlist.txt" # # REQUIRED: For GWAS, GENE, REGIONAL, and VARIANT analyses -- options: [STANDARDIZE/RAW] -STANDARDIZE="STANDARDIZE" -# You can choose one of these options [expected/score] -- expected is likely best; refer to SNPTEST documentation. +STANDARDIZE="RAW" +# REQUIRED: You can choose one of these method options [expected/score] -- expected is likely best; +# refer to SNPTEST documentation and more method options. METHOD="expected" +# REQUIRED: You can indicate to condition on a (list of) variant(s) [NORMAL/CONDITION]; refer to SNPTEST documentation. +CONDITION="CONDITION" +# CONDITIONLIST="${PROJECTDIR}/conditionvariants.rs2521501.txt" +CONDITIONLIST="${PROJECTDIR}/conditionvariants.rs17514846.txt" # # REQUIRED: For GWAS -- make PLINK/this work with VCF files NEW VERSION CLUMP_P2="1"