diff --git a/gwastoolkit.conf b/gwastoolkit.conf
index d2de717..54b0f45 100755
--- a/gwastoolkit.conf
+++ b/gwastoolkit.conf
@@ -8,11 +8,12 @@
 SOFTWARE="/hpc/local/Rocky8/dhl_ec/software"
 
 ### REQUIRED: Path_to where GWASToolKit resides on the server.
-GWASTOOLKITDIR="${SOFTWARE}/GWASToolKit"
+# GWASTOOLKITDIR="${SOFTWARE}/GWASToolKit"
+GWASTOOLKITDIR="/hpc/dhl_ec/tpeters/git_repos/GWASToolKit"
 
 ### REQUIRED: Path_to support programs on the server
 SNPTEST="${SOFTWARE}/snptest_v2.5.4"
-PLINK2="${SOFTWARE}/plink19"
+PLINK2="${SOFTWARE}/plink2"
 LOCUSZOOM13="${SOFTWARE}/locuszoom_1.3/bin/locuszoom"
 
 ### REQUIRED: SLURM settings -- these should work universally
@@ -63,20 +64,22 @@ QTIMEGENECLEANER="01:00:00" # 1hours to clean
 ### 'FAIL' Mail is sent when the job fails.
 ### 'REQUEUE' Mail is sent when the job is re-queued;
 ### 'ALL' Mail sent for all the above.
-YOUREMAIL="s.w.vanderlaan-2@umcutrecht.nl"
+YOUREMAIL="t.s.peters-4@umcutrecht.nl"
 MAILSETTINGS="FAIL"
 
 
 ### ANALYSIS SETTINGS
 ### REQUIRED: Path_to where the main analysis directory resides. Make sure that it exists
-PROJECTDIR="/hpc/dhl_ec/projects/SOMEDIR"
+PROJECTDIR="/hpc/dhl_ec/tpeters/git_repos/GWASToolKit/test_output"
 
 ### REQUIRED: Name of the project, this will automatically be made.
-PROJECTNAME="SOME_FANCY_PROJECTNAME"
+PROJECTNAME="test_project"
 
 ### REQUIRED: Analysis settings.
 ### You can choose one of these options [GWAS/VARIANT/REGION/GENES].
-ANALYSIS_TYPE="VARIANT"
+ANALYSIS_TYPE="GWAS"
+### You can choose one of these options if GWAS is chosen [SNPTEST/REGENIE]
+GWAS_TYPE="REGENIE"
 ### You can choose one of these options [AEGS/AAAGS/CTMM/UCORBIO/MYOMARKER/HELPFULL/RIVM].
 STUDY_TYPE="AEGS"
 
@@ -103,7 +106,8 @@ PHENOTYPE_FILE="${PROJECTDIR}/phenotypes.txt"
 #
 ### AEGS, TOPMed r3, f10, b38 - vcf.gz files 
 # (note that b38 codes chromosomes as 'chr[#]', for example 'chr1')
-IMPUTEDDATA="/hpc/dhl_ec/data/_ae_originals/AEGS_QC_imputation_2023/aegscombo/_topmed_r3_f10_b38/aegscombo.topmed_r3_f10_b38.split_norm_af_filter.chr"
+# IMPUTEDDATA="/hpc/dhl_ec/data/_ae_originals/AEGS_QC_imputation_2023/aegscombo/_topmed_r3_f10_b38/aegscombo.topmed_r3_f10_b38.split_norm_af_filter.chr"
+IMPUTEDDATA="/hpc/dhl_ec/tpeters/regenie_pgen/converted/aegscombo_topmed_r3_f10_b38.chr"
 
 ### AAAGS, 1000G phase 3, GoNL5
 # IMPUTEDDATA="/hpc/dhl_ec/data/_aaa_originals/AAAGS_IMPUTE2_1000Gp3_GoNL5/aaags_1kGp3GoNL5_RAW_chr"
@@ -127,7 +131,7 @@ IMPUTEDDATA="/hpc/dhl_ec/data/_ae_originals/AEGS_QC_imputation_2023/aegscombo/_t
 # SAMPLE_FILE="${PROJECTDIR}/20230523.PCSK9.AEGS123.males.sample"
 # SAMPLE_FILE="${PROJECTDIR}/20230523.PCSK9.AEGS123.sample"
 # SAMPLE_FILE_CHRX="${PROJECTDIR}/20230523.PCSK9.AEGS123.chrX.sample"
-SAMPLE_FILE="${PROJECTDIR}/20240531.PCSK9.AEGS123.sample"
+SAMPLE_FILE="/hpc/dhl_ec/tpeters/regenie_pgen/20240905.IPH_Binary.AEGS123.pheno"
 
 ### AAAGS
 # SAMPLE_FILE="/hpc/dhl_ec/data/_aaa_originals/pheno_cov_exclusions/aaags_phenocov.sample"
@@ -222,3 +226,35 @@ REFERENCEDATA="${GWASTOOLKITDIR}/RESOURCES/1000Gp3v5_EUR/1000Gp3v5.20130502.EUR"
 ### - GENCODE based: gencode_v19_GRCh37_hg19_Feb2009.txt.gz
 ### - PLINK-style gene list: glist-hg19.gz
 HG19_GENES="${GWASTOOLKITDIR}/RESOURCES/glist-hg19.gz"
+
+
+# REGENIE Addition
+REGENIE="${SOFTWARE}/mambaforge3/envs/gwasregenie/bin/regenie"
+
+REGENIE_CALL_RATE="0.10" # PLINK call rate with the flag --geno
+REGENIE_MAF="0.10" # PLINK MAF with the flag --maf
+REGENIE_HWE="1e-3" # PLINK Hardy-Weinberg Equilibrium (HWE) with the flag --hwe
+REGENIE_PRUNE="100 10 0.2" #Prune the data to only select independent SNPs (with low LD r^2) of one pair each with r^2 = 0.2 with the flags --indep-pairwise
+
+REGENIE_STEP1_BZISE="1000"
+REGENIE_STEP2_BZISE="1000"
+
+IMPUTEDDATA_ALLCHR="/hpc/dhl_ec/tpeters/regenie_pgen/OUT/aegscombo_topmed_r3_f10_b38.allChrs"
+
+QMEMGWASREGENIE="16G" # '8Gb' for GWAS Regenie
+QTIMEGWASREGENIE="00:15:00" # 12 hours for GWAS Regenie
+QMEMGWASREGENIE1="64G" # '8Gb' for GWAS Regenie
+QTIMEGWASREGENIE1="2:00:00" # 12 hours for GWAS Regenie
+QMEMGWASREGENIE2="64G" # '8Gb' for GWAS Regenie
+QTIMEGWASREGENIE2="8:00:00" # 12 hours for GWAS Regenie
+QMEMGWASREGENIEWRAP="16G" # '8Gb' for GWAS Regenie
+QTIMEGWASREGENIEWRAP="00:15:00" # 12 hours for GWAS Regenie
+
+EXCLUDE_RANGE_FILE="/hpc/dhl_ec/tpeters/regenie_pgen/exclude_problematic_range_b38.txt"
+
+COVARIATE_QUANTATIVE="Age,PC1,PC2,ORyear"
+COVARIATE_BINARY="SEX"
+# PHENOTYPE_QUANTATIVE="IPH_CLAM_prob,IPH_CLAM_area,IPH_CLAM_prob_rankNorm,IPH_CLAM_area_rankNorm"
+# PHENOTYPE_QUANTATIVE=""
+PHENOTYPE_BINARY="IPH,IPH_CLAM"
+# PHENOTYPE_BINARY=""
diff --git a/gwastoolkit.regenie.qc.sh b/gwastoolkit.regenie.qc.sh
new file mode 100755
index 0000000..cdfcea0
--- /dev/null
+++ b/gwastoolkit.regenie.qc.sh
@@ -0,0 +1,190 @@
+#!/bin/bash
+
+### Creating display functions
+### Setting colouring
+NONE='\033[00m'
+OPAQUE='\033[2m'
+FLASHING='\033[5m'
+BOLD='\033[1m'
+ITALIC='\033[3m'
+UNDERLINE='\033[4m'
+STRIKETHROUGH='\033[9m'
+
+RED='\033[01;31m'
+GREEN='\033[01;32m'
+YELLOW='\033[01;33m'
+PURPLE='\033[01;35m'
+CYAN='\033[01;36m'
+WHITE='\033[01;37m'
+
+function echobold { #'echobold' is the function name
+    echo -e "${BOLD}${1}${NONE}" # this is whatever the function needs to execute, note ${1} is the text for echo
+}
+function echoitalic {
+    echo -e "${ITALIC}${1}${NONE}"
+}
+function echonooption {
+    echo -e "${OPAQUE}${RED}${1}${NONE}"
+}
+function echoerrorflash {
+    echo -e "${RED}${BOLD}${FLASHING}${1}${NONE}"
+}
+function echoerror {
+    echo -e "${RED}${1}${NONE}"
+}
+# errors no option
+function echoerrornooption {
+    echo -e "${YELLOW}${1}${NONE}"
+}
+function echoerrorflashnooption {
+    echo -e "${YELLOW}${BOLD}${FLASHING}${1}${NONE}"
+}
+
+### MESSAGE FUNCTIONS
+script_copyright_message() {
+	echo ""
+	THISYEAR=$(date +'%Y')
+	echo "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
+	echo "+ The MIT License (MIT)                                                                                 +"
+	echo "+ Copyright (c) 2015-${THISYEAR} Tim S. Peters                                                          +"
+	echo "+                                                                                                       +"
+	echo "+ Permission is hereby granted, free of charge, to any person obtaining a copy of this software and     +"
+	echo "+ associated documentation files (the \"Software\"), to deal in the Software without restriction,         +"
+	echo "+ including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, +"
+	echo "+ and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, +"
+	echo "+ subject to the following conditions:                                                                  +"
+	echo "+                                                                                                       +"
+	echo "+ The above copyright notice and this permission notice shall be included in all copies or substantial  +"
+	echo "+ portions of the Software.                                                                             +"
+	echo "+                                                                                                       +"
+	echo "+ THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT     +"
+	echo "+ NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND                +"
+	echo "+ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES  +"
+	echo "+ OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN   +"
+	echo "+ CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.                            +"
+	echo "+                                                                                                       +"
+	echo "+ Reference: http://opensource.org.                                                                     +"
+	echo "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
+}
+script_arguments_error() {
+	echoerror "$1" # ERROR MESSAGE
+	echoerror ""
+	echoerror "- Argument #1 is path_to the configuration file."
+	echoerror ""
+	echoerror "An example command would be: gwastoolkit.regenie.qc.sh [arg1: path_to_configuration_file]"
+  	echoerror ""
+  	echoerror "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
+  	# The wrong arguments are passed, so we'll exit the script now!
+  	exit 1
+}
+
+echobold "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
+echobold "                                         GWASTOOLKIT QUALITY CONTROL for REGENIE"
+echobold "                                 quality control of REGENIE analysis results"
+echobold ""
+echobold " Version    : v1.0.0"
+echobold ""
+echobold " Last update: 2024-08-29"
+echobold " Written by :  Tim S. Peters (t.s.peters-4@umcutrecht.nl)."
+echobold ""
+echobold " Testers:     - "
+echobold ""
+echobold " Description: Quality control of a REGENIE analysis:"
+echobold " Filter on:	- autosome snps"
+echobold " 				- MAF"
+echobold " 				- MAC"
+echobold " 				- call rate"
+echobold " 				- Hardy-Weinberg Equilibrium (HWE) p-value"
+echobold " 				- LD r^2"
+echobold " 				- exclude problamatic SNPs in long-range LD regions"
+echobold ""
+echobold "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
+
+### LOADING CONFIGURATION FILE
+source "$1" # Depends on arg1.
+
+### REQUIRED | GENERALS
+CONFIGURATIONFILE="$1" # Depends on arg1 -- but also on where it resides!!!
+
+### START of if-else statement for the number of command-line arguments passed ###
+if [[ $# -lt 1 ]]; then
+	echo "Oh, computer says no! Number of arguments found "$#"."
+	script_arguments_error "You must supply [1] argument for cleaning of *** GENOME-WIDE ANALYSIS *** results!"
+	script_copyright_message
+
+else
+	### Make and/or set the output directory
+	if [ ! -d ${PROJECTDIR}/${PROJECTNAME}/regenie_results ]; then
+		echo "The output directory does not exist. Making and setting it."
+		mkdir -v ${PROJECTDIR}/${PROJECTNAME}/regenie_results
+		OUTPUT_DIR=${PROJECTDIR}/${PROJECTNAME}/regenie_results
+	else
+		echo "The output directory already exists. Setting it."
+		OUTPUT_DIR=${PROJECTDIR}/${PROJECTNAME}/regenie_results
+	fi
+
+	if [ ! -d ${OUTPUT_DIR}/pre_processing ]; then
+		echo "The QC output directory does not exist. Making and setting it."
+		mkdir -v ${OUTPUT_DIR}/pre_processing
+		QC_OUTPUT_DIR=${OUTPUT_DIR}/pre_processing
+	else
+		echo "The QC output directory already exists. Setting it."
+		QC_OUTPUT_DIR=${OUTPUT_DIR}/pre_processing
+	fi
+
+	echo "All arguments are passed. These are the settings:"
+	echo "The output directory is...................: ${OUTPUT_DIR}"
+	echo "The call rate filter is...................: ${REGENIE_CALL_RATE}"
+	echo "The minimum minor allele frequency is.....: ${REGENIE_MAF}"
+	echo "The minimum HWE p-value is................: ${REGENIE_HWE}"
+	echo "The filter for independent SNPs is........: ${REGENIE_PRUNE}"
+	echo ""
+	# PLOT GWAS RESULTS
+	echo "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
+	echo "                                            STARTING QUALITY CONTROL"
+	echo ""
+	echo "Please be patient...this can take a long time depending on the number of files."
+	echo "We started at: "$(date)
+	echo ""
+	echo ""
+	echo "First, get a list of A/T and C/G SNPs, to exclude later:"
+	cat ${IMPUTEDDATA_ALLCHR}.pvar | \
+	awk '($4 == "A" && $5 == "T") || ($4 == "T" && $5 == "A") || ($4 == "C" && $5 == "G") || ($4 == "G" && $5 == "C")' | \
+	awk '{ print $3, $1, $2, 0, $4, $5 }' > ${QC_OUTPUT_DIR}/all.atcg.variants.txt
+	echo ""
+	echo ""
+	echo "Second, filtering data, using the following criteria: "
+	echo "  * CALL RATE < ${REGENIE_CALL_RATE}"
+	echo "  * MAF >= ${REGENIE_MAF}"
+	echo "  * HWE <= ${REGENIE_HWE}"
+	echo "  * indep_pairwise ${REGENIE_PRUNE}"
+	$PLINK2 --pfile ${IMPUTEDDATA_ALLCHR} \
+	--autosome \
+	--maf ${REGENIE_MAF} --geno ${REGENIE_CALL_RATE} --hwe ${REGENIE_HWE} \
+	--exclude-if-info "R2>0.99" \
+	--indep-pairwise ${REGENIE_PRUNE}\
+	--exclude range ${EXCLUDE_RANGE_FILE} \
+	--make-pgen --out ${QC_OUTPUT_DIR}/aegscombo_topmed_r3_f10_b38.allChrs.temp
+	echo ""
+	echo ""
+	echo "Third, prune out unwanted SNPs in high LD."
+	$PLINK2 --pfile ${QC_OUTPUT_DIR}/aegscombo_topmed_r3_f10_b38.allChrs.temp \
+	--extract ${QC_OUTPUT_DIR}/aegscombo_topmed_r3_f10_b38.allChrs.temp.prune.in \
+	--make-pgen --out ${QC_OUTPUT_DIR}/aegscombo_topmed_r3_f10_b38.allChrs.ultraclean.temp
+	echo ""
+	echo ""
+	echo "Fourth, remove the A/T and C/G SNPs."
+	$PLINK2 --pfile ${QC_OUTPUT_DIR}/aegscombo_topmed_r3_f10_b38.allChrs.ultraclean.temp \
+	--exclude ${QC_OUTPUT_DIR}/all.atcg.variants.txt \
+	--write-snplist --write-samples --no-id-header \
+	--make-pgen --out ${QC_OUTPUT_DIR}/aegscombo_topmed_r3_f10_b38.allChrs.QC
+	echo ""
+	echo ""
+	echo "Finishing up..."
+	rm -fv ${QC_OUTPUT_DIR}/*.temp*
+	echo ""
+	echo ""
+### END of if-else statement for the number of command-line arguments passed ###
+fi
+
+# script_copyright_message
diff --git a/gwastoolkit.regenie.step1.sh b/gwastoolkit.regenie.step1.sh
new file mode 100755
index 0000000..d05eab0
--- /dev/null
+++ b/gwastoolkit.regenie.step1.sh
@@ -0,0 +1,244 @@
+#!/bin/bash
+
+### Creating display functions
+### Setting colouring
+NONE='\033[00m'
+OPAQUE='\033[2m'
+FLASHING='\033[5m'
+BOLD='\033[1m'
+ITALIC='\033[3m'
+UNDERLINE='\033[4m'
+STRIKETHROUGH='\033[9m'
+
+RED='\033[01;31m'
+GREEN='\033[01;32m'
+YELLOW='\033[01;33m'
+PURPLE='\033[01;35m'
+CYAN='\033[01;36m'
+WHITE='\033[01;37m'
+
+function echobold { #'echobold' is the function name
+    echo -e "${BOLD}${1}${NONE}" # this is whatever the function needs to execute, note ${1} is the text for echo
+}
+function echoitalic {
+    echo -e "${ITALIC}${1}${NONE}"
+}
+function echonooption {
+    echo -e "${OPAQUE}${RED}${1}${NONE}"
+}
+function echoerrorflash {
+    echo -e "${RED}${BOLD}${FLASHING}${1}${NONE}"
+}
+function echoerror {
+    echo -e "${RED}${1}${NONE}"
+}
+# errors no option
+function echoerrornooption {
+    echo -e "${YELLOW}${1}${NONE}"
+}
+function echoerrorflashnooption {
+    echo -e "${YELLOW}${BOLD}${FLASHING}${1}${NONE}"
+}
+
+### MESSAGE FUNCTIONS
+script_copyright_message() {
+	echo ""
+	THISYEAR=$(date +'%Y')
+	echo "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
+	echo "+ The MIT License (MIT)                                                                                 +"
+	echo "+ Copyright (c) 2015-${THISYEAR} Tim S. Peters                                                          +"
+	echo "+                                                                                                       +"
+	echo "+ Permission is hereby granted, free of charge, to any person obtaining a copy of this software and     +"
+	echo "+ associated documentation files (the \"Software\"), to deal in the Software without restriction,         +"
+	echo "+ including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, +"
+	echo "+ and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, +"
+	echo "+ subject to the following conditions:                                                                  +"
+	echo "+                                                                                                       +"
+	echo "+ The above copyright notice and this permission notice shall be included in all copies or substantial  +"
+	echo "+ portions of the Software.                                                                             +"
+	echo "+                                                                                                       +"
+	echo "+ THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT     +"
+	echo "+ NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND                +"
+	echo "+ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES  +"
+	echo "+ OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN   +"
+	echo "+ CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.                            +"
+	echo "+                                                                                                       +"
+	echo "+ Reference: http://opensource.org.                                                                     +"
+	echo "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
+}
+script_arguments_error() {
+	echoerror "$1" # ERROR MESSAGE
+	echoerror ""
+	echoerror "- Argument #1 is path_to the configuration file."
+	echoerror "- Argument #2 is determining whether to run regenie for BINARY or QUANTATIVE traits."
+	echoerror ""
+	echoerror "An example command would be: gwastoolkit.regenie.step1.sh [arg1: path_to_configuration_file] [args2: BINARY/QUANTATIVE]"
+  	echoerror ""
+  	echoerror "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
+  	# The wrong arguments are passed, so we'll exit the script now!
+  	exit 1
+}
+
+echobold "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
+echobold "                                         GWASTOOLKIT REGENIE STEP 1"
+echobold "                                         step 1 of REGENIE analysis"
+echobold ""
+echobold " Version    : v1.0.0"
+echobold ""
+echobold " Last update: 2024-08-29"
+echobold " Written by :  Tim S. Peters (t.s.peters-4@umcutrecht.nl)."
+echobold ""
+echobold " Testers:     - "
+echobold ""
+echobold " Description: First step of GWAS using Regenie:"
+echobold " Filter on:	- autosome snps"
+echobold " 				- MAF"
+echobold " 				- MAC"
+echobold " 				- call rate"
+echobold " 				- Hardy-Weinberg Equilibrium (HWE) p-value"
+echobold " 				- LD r^2"
+echobold " 				- exclude problamatic SNPs in long-range LD regions"
+echobold ""
+echobold "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
+
+### LOADING CONFIGURATION FILE
+source "$1" # Depends on arg1.
+
+### REQUIRED | GENERALS
+CONFIGURATIONFILE="$1" # Depends on arg1 -- but also on where it resides!!!
+TRAIT_TYPE="$2" # Depends on arg1 -- but also on where it resides!!!
+
+### START of if-else statement for the number of command-line arguments passed ###
+if [[ $# -lt 2 ]]; then
+	echo "Oh, computer says no! Number of arguments found "$#"."
+	script_arguments_error "You must supply [2] arguments for cleaning of *** GENOME-WIDE ANALYSIS *** results!"
+	script_copyright_message
+
+else
+	if [[ "${TRAIT_TYPE}" != 'BINARY' && "${TRAIT_TYPE}" != 'QUANTATIVE' ]]; then
+		echo "Oh, computer says no! Second argument is not correct"
+		script_arguments_error "Argument 2 should be either 'BINARY' or 'QUANTATIVE'!"
+		script_copyright_message
+		exit 1
+	fi
+	echo ""
+	echo ""
+	### Make and/or set the output directory
+	if [ ! -d ${PROJECTDIR}/${PROJECTNAME}/regenie_results ]; then
+		echo "The output directory does not exist. Making and setting it."
+		mkdir -v ${PROJECTDIR}/${PROJECTNAME}/regenie_results
+		OUTPUT_DIR=${PROJECTDIR}/${PROJECTNAME}/regenie_results
+	else
+		echo "The output directory already exists. Setting it."
+		OUTPUT_DIR=${PROJECTDIR}/${PROJECTNAME}/regenie_results
+	fi
+	echo ""
+
+	if [ ! -d ${OUTPUT_DIR}/pre_processing ]; then
+		echo "The QC output directory does not exist. Making and setting it."
+		echo "Something probably went wrong in the QC step."
+		exit 1
+	else
+		echo "The QC output directory exists. Setting it."
+		QC_OUTPUT_DIR=${OUTPUT_DIR}/pre_processing
+	fi
+	echo ""
+
+	if [ "${TRAIT_TYPE}" == 'QUANTATIVE' ]; then
+		echo "* Running REGENIE for QUANTATIVE traits"
+		if [ ! -d ${OUTPUT_DIR}/regenie_QT_step1 ]; then
+			echo "The Regenie Quantative traits step1 output directory does not exist. Making and setting it."
+			mkdir -v ${OUTPUT_DIR}/regenie_QT_step1
+			STEP1_QT_OUTPUT_DIR=${OUTPUT_DIR}/regenie_QT_step1
+		else
+			echo "The Regenie Quantative traits step1 output directory already exists. Setting it."
+			STEP1_QT_OUTPUT_DIR=${OUTPUT_DIR}/regenie_QT_step1
+		fi
+		echo ""
+	fi
+
+	if [ "${TRAIT_TYPE}" == 'BINARY' ]; then
+		echo "* Running REGENIE for BINARY traits"
+		if [ ! -d ${OUTPUT_DIR}/regenie_BT_step1 ]; then
+			echo "The Regenie Binary traits step1 output directory does not exist. Making and setting it."
+			mkdir -v ${OUTPUT_DIR}/regenie_BT_step1
+			STEP1_BT_OUTPUT_DIR=${OUTPUT_DIR}/regenie_BT_step1
+		else
+			echo "The Regenie Binary traits step1 output directory already exists. Setting it."
+			STEP1_BT_OUTPUT_DIR=${OUTPUT_DIR}/regenie_BT_step1
+		fi
+		echo ""
+	fi
+
+	if [ ! -d ${OUTPUT_DIR}/tmp_dir ]; then
+		echo "The temporary directory does not exist. Making and setting it."
+		mkdir -v ${OUTPUT_DIR}/tmp_dir
+		TMP_OUTPUT_DIR=${OUTPUT_DIR}/tmp_dir
+	else
+		echo "The temporary directory already exists. Setting it."
+		TMP_OUTPUT_DIR=${OUTPUT_DIR}/tmp_dir
+	fi
+	echo ""
+	echo ""
+
+	if [ "${TRAIT_TYPE}" == 'QUANTATIVE' ]; then	
+		echo "All arguments are passed. These are the settings:"
+		echo "  * SAMPLE FILE: 				${SAMPLE_FILE}"
+		echo "  * QUANTATIVE COVARIATES: 	${COVARIATE_QUANTATIVE}"
+		echo "  * BINARY COVARIATES: 		${COVARIATE_BINARY}"
+		echo "  * QUANTATIVE PHENOTYPE: 	${PHENOTYPE_QUANTATIVE}"
+		echo "  * BINARY PHENOTYPE: 		-NOT USED-"
+		echo ""
+		echo "  * BLOCK SIZE: 				${REGENIE_STEP1_BZISE}"
+		echo ""
+		echo ""
+		echo "Start processing REGENIE step 1 for QUANTATIVE traits"
+		echo ""
+		$REGENIE \
+		--step 1 \
+		--pgen ${QC_OUTPUT_DIR}/aegscombo_topmed_r3_f10_b38.allChrs.QC \
+		--extract ${QC_OUTPUT_DIR}/aegscombo_topmed_r3_f10_b38.allChrs.QC.snplist \
+		--keep ${QC_OUTPUT_DIR}/aegscombo_topmed_r3_f10_b38.allChrs.QC.id \
+		--covarFile ${SAMPLE_FILE} \
+		--covarColList ${COVARIATE_QUANTATIVE} \
+		--catCovarList ${COVARIATE_BINARY} \
+		--phenoFile ${SAMPLE_FILE} \
+		--phenoColList ${PHENOTYPE_QUANTATIVE} \
+		--bsize="${REGENIE_STEP1_BZISE}" \
+		--lowmem \
+		--lowmem-prefix ${TMP_OUTPUT_DIR}/regenie_tmp_qt_preds \
+		--out ${STEP1_QT_OUTPUT_DIR}/aegscombo_topmed_step1
+		
+	elif [ "${TRAIT_TYPE}" == 'BINARY' ]; then
+		echo "All arguments are passed. These are the settings:"
+		echo "  * SAMPLE FILE: 				${SAMPLE_FILE}"
+		echo "  * QUANTATIVE COVARIATES: 	${COVARIATE_QUANTATIVE}"
+		echo "  * BINARY COVARIATES: 		${COVARIATE_BINARY}"
+		echo "  * QUANTATIVE PHENOTYPE: 	-NOT USED-"
+		echo "  * BINARY PHENOTYPE: 		${PHENOTYPE_BINARY}"
+		echo ""
+		echo "  * BLOCK SIZE: 				${REGENIE_STEP1_BZISE}"
+		echo ""
+		echo ""
+		echo "Start processing REGENIE step 1 for BINARY traits"
+		echo ""
+		$REGENIE \
+		--step 1 \
+		--pgen ${QC_OUTPUT_DIR}/aegscombo_topmed_r3_f10_b38.allChrs.QC \
+		--extract ${QC_OUTPUT_DIR}/aegscombo_topmed_r3_f10_b38.allChrs.QC.snplist \
+		--keep ${QC_OUTPUT_DIR}/aegscombo_topmed_r3_f10_b38.allChrs.QC.id \
+		--covarFile ${SAMPLE_FILE} \
+		--covarColList ${COVARIATE_QUANTATIVE} \
+		--catCovarList ${COVARIATE_BINARY} \
+		--phenoFile ${SAMPLE_FILE} \
+		--phenoColList ${PHENOTYPE_BINARY} \
+		--bsize="${REGENIE_STEP1_BZISE}" \
+		--lowmem --bt \
+		--lowmem-prefix ${TMP_OUTPUT_DIR}/regenie_tmp_bt_preds \
+		--out ${STEP1_BT_OUTPUT_DIR}/aegscombo_topmed_step1
+	fi
+
+### END of if-else statement for the number of command-line arguments passed ###
+fi
+
+# script_copyright_message
diff --git a/gwastoolkit.regenie.step2.sh b/gwastoolkit.regenie.step2.sh
new file mode 100755
index 0000000..c4704ee
--- /dev/null
+++ b/gwastoolkit.regenie.step2.sh
@@ -0,0 +1,234 @@
+#!/bin/bash
+
+### Creating display functions
+### Setting colouring
+NONE='\033[00m'
+OPAQUE='\033[2m'
+FLASHING='\033[5m'
+BOLD='\033[1m'
+ITALIC='\033[3m'
+UNDERLINE='\033[4m'
+STRIKETHROUGH='\033[9m'
+
+RED='\033[01;31m'
+GREEN='\033[01;32m'
+YELLOW='\033[01;33m'
+PURPLE='\033[01;35m'
+CYAN='\033[01;36m'
+WHITE='\033[01;37m'
+
+function echobold { #'echobold' is the function name
+    echo -e "${BOLD}${1}${NONE}" # this is whatever the function needs to execute, note ${1} is the text for echo
+}
+function echoitalic {
+    echo -e "${ITALIC}${1}${NONE}"
+}
+function echonooption {
+    echo -e "${OPAQUE}${RED}${1}${NONE}"
+}
+function echoerrorflash {
+    echo -e "${RED}${BOLD}${FLASHING}${1}${NONE}"
+}
+function echoerror {
+    echo -e "${RED}${1}${NONE}"
+}
+# errors no option
+function echoerrornooption {
+    echo -e "${YELLOW}${1}${NONE}"
+}
+function echoerrorflashnooption {
+    echo -e "${YELLOW}${BOLD}${FLASHING}${1}${NONE}"
+}
+
+### MESSAGE FUNCTIONS
+script_copyright_message() {
+	echo ""
+	THISYEAR=$(date +'%Y')
+	echo "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
+	echo "+ The MIT License (MIT)                                                                                 +"
+	echo "+ Copyright (c) 2015-${THISYEAR} Tim S. Peters                                                          +"
+	echo "+                                                                                                       +"
+	echo "+ Permission is hereby granted, free of charge, to any person obtaining a copy of this software and     +"
+	echo "+ associated documentation files (the \"Software\"), to deal in the Software without restriction,         +"
+	echo "+ including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, +"
+	echo "+ and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, +"
+	echo "+ subject to the following conditions:                                                                  +"
+	echo "+                                                                                                       +"
+	echo "+ The above copyright notice and this permission notice shall be included in all copies or substantial  +"
+	echo "+ portions of the Software.                                                                             +"
+	echo "+                                                                                                       +"
+	echo "+ THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT     +"
+	echo "+ NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND                +"
+	echo "+ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES  +"
+	echo "+ OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN   +"
+	echo "+ CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.                            +"
+	echo "+                                                                                                       +"
+	echo "+ Reference: http://opensource.org.                                                                     +"
+	echo "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
+}
+script_arguments_error() {
+	echoerror "$1" # ERROR MESSAGE
+	echoerror ""
+	echoerror "- Argument #1 is path_to the configuration file."
+	echoerror "- Argument #2 is determining whether to run regenie for BINARY or QUANTATIVE traits."
+	echoerror ""
+	echoerror "An example command would be: gwastoolkit.regenie.step2.sh [arg1: path_to_configuration_file] [args2: BINARY/QUANTATIVE]"
+  	echoerror ""
+  	echoerror "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
+  	# The wrong arguments are passed, so we'll exit the script now!
+  	exit 1
+}
+
+echobold "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
+echobold "                                         GWASTOOLKIT REGENIE STEP 2"
+echobold "                                         step 2 of REGENIE analysis"
+echobold ""
+echobold " Version    : v1.0.0"
+echobold ""
+echobold " Last update: 2024-08-29"
+echobold " Written by :  Tim S. Peters (t.s.peters-4@umcutrecht.nl)."
+echobold ""
+echobold " Testers:     - "
+echobold ""
+echobold ""
+echobold "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
+
+### LOADING CONFIGURATION FILE
+source "$1" # Depends on arg1.
+
+### REQUIRED | GENERALS
+CONFIGURATIONFILE="$1" # Depends on arg1 -- but also on where it resides!!!
+TRAIT_TYPE="$2" # Depends on arg1 -- but also on where it resides!!!
+
+### START of if-else statement for the number of command-line arguments passed ###
+if [[ $# -lt 2 ]]; then
+	echo "Oh, computer says no! Number of arguments found "$#"."
+	script_arguments_error "You must supply [2] arguments for cleaning of *** GENOME-WIDE ANALYSIS *** results!"
+	script_copyright_message
+
+else
+	if [[ "${TRAIT_TYPE}" != 'BINARY' && "${TRAIT_TYPE}" != 'QUANTATIVE' ]]; then
+		echo "Oh, computer says no! Second argument is not correct"
+		script_arguments_error "Argument 2 should be either 'BINARY' or 'QUANTATIVE'!"
+		script_copyright_message
+		exit 1
+	fi
+	echo ""
+	echo ""
+	### Make and/or set the output directory
+	if [ ! -d ${PROJECTDIR}/${PROJECTNAME}/regenie_results ]; then
+		echo "The output directory does not exist. Making and setting it."
+		mkdir -v ${PROJECTDIR}/${PROJECTNAME}/regenie_results
+		OUTPUT_DIR=${PROJECTDIR}/${PROJECTNAME}/regenie_results
+	else
+		echo "The output directory already exists. Setting it."
+		OUTPUT_DIR=${PROJECTDIR}/${PROJECTNAME}/regenie_results
+	fi
+	echo ""
+
+	if [ "${TRAIT_TYPE}" == 'QUANTATIVE' ]; then
+		echo "* Running REGENIE for QUANTATIVE traits"
+		if [ ! -d ${OUTPUT_DIR}/regenie_QT_step2 ]; then
+			echo "The Regenie Quantative traits step2 output directory does not exist. Making and setting it."
+			mkdir -v ${OUTPUT_DIR}/regenie_QT_step2
+			STEP2_QT_OUTPUT_DIR=${OUTPUT_DIR}/regenie_QT_step2
+		else
+			echo "The Regenie Quantative traits step2 output directory already exists. Setting it."
+			STEP2_QT_OUTPUT_DIR=${OUTPUT_DIR}/regenie_QT_step2
+		fi
+		echo ""
+
+		if [ ! -d ${OUTPUT_DIR}/regenie_QT_step1 ]; then
+			script_arguments_error "Regenie step 1 does not seem to be executed or the directory could not be found!"
+			script_copyright_message
+			exit 1
+		else
+			echo "The Regenie Quantative traits step1 output directory exists. Setting it."
+			STEP1_QT_OUTPUT_DIR=${OUTPUT_DIR}/regenie_QT_step1
+		fi
+		echo ""
+	fi
+
+	if [ "${TRAIT_TYPE}" == 'BINARY' ]; then
+		echo "* Running REGENIE for BINARY traits"
+		if [ ! -d ${OUTPUT_DIR}/regenie_BT_step2 ]; then
+			echo "The Regenie Binary traits step2 output directory does not exist. Making and setting it."
+			mkdir -v ${OUTPUT_DIR}/regenie_BT_step2
+			STEP2_BT_OUTPUT_DIR=${OUTPUT_DIR}/regenie_BT_step2
+		else
+			echo "The Regenie Binary traits step2 output directory already exists. Setting it."
+			STEP2_BT_OUTPUT_DIR=${OUTPUT_DIR}/regenie_BT_step2
+		fi
+		echo ""
+
+		if [ ! -d ${OUTPUT_DIR}/regenie_BT_step1 ]; then
+			script_arguments_error "Regenie step 1 does not seem to be executed or the directory could not be found!"
+			script_copyright_message
+			exit 1
+		else
+			echo "The Regenie Binary traits step1 output directory exists. Setting it."
+			STEP1_BT_OUTPUT_DIR=${OUTPUT_DIR}/regenie_BT_step1
+		fi
+		echo ""
+	fi
+
+	echo ""
+
+	if [ "${TRAIT_TYPE}" == 'QUANTATIVE' ]; then	
+		echo "All arguments are passed. These are the settings:"
+		echo "  * SAMPLE FILE: 				${SAMPLE_FILE}"
+		echo "  * QUANTATIVE COVARIATES: 	${COVARIATE_QUANTATIVE}"
+		echo "  * BINARY COVARIATES: 		${COVARIATE_BINARY}"
+		echo "  * QUANTATIVE PHENOTYPE: 	${PHENOTYPE_QUANTATIVE}"
+		echo "  * BINARY PHENOTYPE: 		-NOT USED-"
+		echo ""
+		echo "  * BLOCK SIZE: 				${REGENIE_STEP2_BZISE}"
+		echo ""
+		echo ""
+		echo "Start processing REGENIE step 2 for QUANTATIVE traits"
+		echo ""
+		for chr in {1..22}; do $REGENIE \
+		--step 2 \
+		--pgen ${IMPUTEDDATA}${chr} \
+		--covarFile ${SAMPLE_FILE} \
+		--covarColList ${COVARIATE_QUANTATIVE} \
+		--catCovarList ${COVARIATE_BINARY} \
+		--phenoFile ${SAMPLE_FILE} \
+		--phenoColList ${PHENOTYPE_QUANTATIVE} \
+		--firth --approx --pThresh 0.01\
+		--pred ${STEP1_QT_OUTPUT_DIR}/aegscombo_topmed_step1_pred.list \
+		--bsize="${REGENIE_STEP2_BZISE}" \
+		--out ${STEP2_QT_OUTPUT_DIR}/aegscombo_step2_topmed_r3_f10_b38.chr${chr}; done
+		
+	elif [ "${TRAIT_TYPE}" == 'BINARY' ]; then
+		echo "All arguments are passed. These are the settings:"
+		echo "  * SAMPLE FILE: 				${SAMPLE_FILE}"
+		echo "  * QUANTATIVE COVARIATES: 	${COVARIATE_QUANTATIVE}"
+		echo "  * BINARY COVARIATES: 		${COVARIATE_BINARY}"
+		echo "  * QUANTATIVE PHENOTYPE: 	-NOT USED-"
+		echo "  * BINARY PHENOTYPE: 		${PHENOTYPE_BINARY}"
+		echo ""
+		echo "  * BLOCK SIZE: 				${REGENIE_STEP2_BZISE}"
+		echo ""
+		echo ""
+		echo "Start processing REGENIE step 2 for BINARY traits"
+		echo ""
+		for chr in {1..22}; do $REGENIE \
+		--step 2 \
+		--pgen ${IMPUTEDDATA}${chr} \
+		--covarFile ${SAMPLE_FILE} \
+		--covarColList ${COVARIATE_QUANTATIVE} \
+		--catCovarList ${COVARIATE_BINARY} \
+		--phenoFile ${SAMPLE_FILE} \
+		--phenoColList ${PHENOTYPE_BINARY} \
+		--firth --approx --pThresh 0.01\
+		--pred ${STEP1_BT_OUTPUT_DIR}/aegscombo_topmed_step1_pred.list \
+		--bsize="${REGENIE_STEP2_BZISE}" \
+		--bt \
+		--out ${STEP2_BT_OUTPUT_DIR}/aegscombo_step2_topmed_r3_f10_b38.chr${chr}; done
+	fi
+
+### END of if-else statement for the number of command-line arguments passed ###
+fi
+
+# script_copyright_message
diff --git a/gwastoolkit.regenie.wrapper.sh b/gwastoolkit.regenie.wrapper.sh
new file mode 100755
index 0000000..c07081d
--- /dev/null
+++ b/gwastoolkit.regenie.wrapper.sh
@@ -0,0 +1,243 @@
+#!/bin/bash
+
+### Creating display functions
+### Setting colouring
+NONE='\033[00m'
+OPAQUE='\033[2m'
+FLASHING='\033[5m'
+BOLD='\033[1m'
+ITALIC='\033[3m'
+UNDERLINE='\033[4m'
+STRIKETHROUGH='\033[9m'
+
+RED='\033[01;31m'
+GREEN='\033[01;32m'
+YELLOW='\033[01;33m'
+PURPLE='\033[01;35m'
+CYAN='\033[01;36m'
+WHITE='\033[01;37m'
+
+function echobold { #'echobold' is the function name
+    echo -e "${BOLD}${1}${NONE}" # this is whatever the function needs to execute, note ${1} is the text for echo
+}
+function echoitalic {
+    echo -e "${ITALIC}${1}${NONE}"
+}
+function echonooption {
+    echo -e "${OPAQUE}${RED}${1}${NONE}"
+}
+function echoerrorflash {
+    echo -e "${RED}${BOLD}${FLASHING}${1}${NONE}"
+}
+function echoerror {
+    echo -e "${RED}${1}${NONE}"
+}
+# errors no option
+function echoerrornooption {
+    echo -e "${YELLOW}${1}${NONE}"
+}
+function echoerrorflashnooption {
+    echo -e "${YELLOW}${BOLD}${FLASHING}${1}${NONE}"
+}
+
+### MESSAGE FUNCTIONS
+script_copyright_message() {
+	echo ""
+	THISYEAR=$(date +'%Y')
+	echo "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
+	echo "+ The MIT License (MIT)                                                                                 +"
+	echo "+ Copyright (c) 2015-${THISYEAR} Tim S. Peters                                                          +"
+	echo "+                                                                                                       +"
+	echo "+ Permission is hereby granted, free of charge, to any person obtaining a copy of this software and     +"
+	echo "+ associated documentation files (the \"Software\"), to deal in the Software without restriction,         +"
+	echo "+ including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, +"
+	echo "+ and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, +"
+	echo "+ subject to the following conditions:                                                                  +"
+	echo "+                                                                                                       +"
+	echo "+ The above copyright notice and this permission notice shall be included in all copies or substantial  +"
+	echo "+ portions of the Software.                                                                             +"
+	echo "+                                                                                                       +"
+	echo "+ THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT     +"
+	echo "+ NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND                +"
+	echo "+ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES  +"
+	echo "+ OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN   +"
+	echo "+ CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.                            +"
+	echo "+                                                                                                       +"
+	echo "+ Reference: http://opensource.org.                                                                     +"
+	echo "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
+}
+script_arguments_error() {
+	echoerror "$1" # ERROR MESSAGE
+	echoerror ""
+	echoerror "- Argument #1 is path_to the configuration file."
+	echoerror "- Argument #2 is determining whether to run regenie for BINARY or QUANTATIVE traits."
+	echoerror ""
+	echoerror "An example command would be: gwastoolkit.regenie.step2.sh [arg1: path_to_configuration_file] [args2: BINARY/QUANTATIVE]"
+  	echoerror ""
+  	echoerror "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
+  	# The wrong arguments are passed, so we'll exit the script now!
+  	exit 1
+}
+
+echobold "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
+echobold "                                         GWASTOOLKIT REGENIE WRAPPER"
+echobold "                                         Wrapup of REGENIE analysis"
+echobold ""
+echobold " Version    : v1.0.0"
+echobold ""
+echobold " Last update: 2024-08-29"
+echobold " Written by :  Tim S. Peters (t.s.peters-4@umcutrecht.nl)."
+echobold ""
+echobold " Testers:     - "
+echobold ""
+echobold ""
+echobold "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
+
+### LOADING CONFIGURATION FILE
+source "$1" # Depends on arg1.
+
+### REQUIRED | GENERALS
+CONFIGURATIONFILE="$1" # Depends on arg1 -- but also on where it resides!!!
+TRAIT_TYPE="$2" # Depends on arg1 -- but also on where it resides!!!
+
+### START of if-else statement for the number of command-line arguments passed ###
+if [[ $# -lt 2 ]]; then
+	echo "Oh, computer says no! Number of arguments found "$#"."
+	script_arguments_error "You must supply [2] arguments for cleaning of *** GENOME-WIDE ANALYSIS *** results!"
+	script_copyright_message
+
+else
+	if [[ "${TRAIT_TYPE}" != 'BINARY' && "${TRAIT_TYPE}" != 'QUANTATIVE' ]]; then
+		echo "Oh, computer says no! Second argument is not correct"
+		script_arguments_error "Argument 2 should be either 'BINARY' or 'QUANTATIVE'!"
+		script_copyright_message
+		exit 1
+	fi
+	echo ""
+	echo ""
+	### Make and/or set the output directory
+	if [ ! -d ${PROJECTDIR}/${PROJECTNAME}/regenie_results ]; then
+		echo "The output directory does not exist. Making and setting it."
+		mkdir -v ${PROJECTDIR}/${PROJECTNAME}/regenie_results
+		OUTPUT_DIR=${PROJECTDIR}/${PROJECTNAME}/regenie_results
+	else
+		echo "The output directory already exists. Setting it."
+		OUTPUT_DIR=${PROJECTDIR}/${PROJECTNAME}/regenie_results
+	fi
+	echo ""
+
+	if [ "${TRAIT_TYPE}" == 'QUANTATIVE' ]; then
+		echo "* Running REGENIE for QUANTATIVE traits"
+		if [ ! -d ${OUTPUT_DIR}/regenie_QT_step2 ]; then
+			script_arguments_error "Regenie step 2 does not seem to be executed or the directory could not be found!"
+			script_copyright_message
+			exit 1
+		else
+			echo "The Regenie Quantative traits step2 output directory already exists. Setting it."
+			STEP2_QT_OUTPUT_DIR=${OUTPUT_DIR}/regenie_QT_step2
+		fi
+		echo ""
+	fi
+
+	if [ "${TRAIT_TYPE}" == 'BINARY' ]; then
+		echo "* Running REGENIE for BINARY traits"
+		if [ ! -d ${OUTPUT_DIR}/regenie_BT_step2 ]; then
+			script_arguments_error "Regenie step 2 does not seem to be executed or the directory could not be found!"
+			script_copyright_message
+			exit 1
+		else
+			echo "The Regenie Binary traits step2 output directory already exists. Setting it."
+			STEP2_BT_OUTPUT_DIR=${OUTPUT_DIR}/regenie_BT_step2
+		fi
+		echo ""
+	fi
+
+	if [ ! -d ${OUTPUT_DIR}/regenie_OUT ]; then
+		echo "The Regenie output directory does not exist. Making and setting it."
+		mkdir -v ${OUTPUT_DIR}/regenie_OUT
+		REGENIE_FINAL_DIR=${OUTPUT_DIR}/regenie_OUT
+	else
+		echo "The Regenie output directory already exists. Setting it."
+		REGENIE_FINAL_DIR=${OUTPUT_DIR}/regenie_OUT
+	fi
+	echo ""
+	echo ""
+
+	# Save the current IFS
+	OLD_IFS=$IFS
+
+	if [ "${TRAIT_TYPE}" == 'QUANTATIVE' ]; then	
+		echo "All arguments are passed. These are the settings:"
+		echo "  * SAMPLE FILE: 				${SAMPLE_FILE}"
+		echo "  * QUANTATIVE COVARIATES: 	${COVARIATE_QUANTATIVE}"
+		echo "  * BINARY COVARIATES: 		${COVARIATE_BINARY}"
+		echo "  * QUANTATIVE PHENOTYPE: 	${PHENOTYPE_QUANTATIVE}"
+		echo "  * BINARY PHENOTYPE: 		-NOT USED-"
+		echo ""
+		echo "  * BLOCK SIZE: 				${REGENIE_STEP2_BZISE}"
+		echo ""
+		echo ""
+		echo "Start processing REGENIE step 2 for QUANTATIVE traits"
+		echo ""
+		
+		IFS=','  # Set comma as the delimiter
+		for PHENOTYPE_ITEM in $PHENOTYPE_QUANTATIVE; do
+			echo "Wrapping up for QUANTATIVE PHENOTYPE: ${PHENOTYPE_ITEM}"
+			# create results file
+			###      1     2    3   4  5            6            7              8    9      10     11     12     CALC 13 CALC 14 15  16 17 # AUTOSOMAL & X CHROMOSOMES
+			# echo "ALTID RSID CHR BP OtherAlleleA CodedAlleleB AvgMaxPostCall Info all_AA all_AB all_BB TotalN MAC MAF CAF HWE P BETA SE" > ${PHENO_OUTPUT_DIR}/${STUDY_TYPE}.${ANALYSIS_TYPE}.${REFERENCE}.${PHENOTYPE}.${EXCLUSION}.summary_results.txt
+			echo "CHROM GENPOS ID ALLELE0 ALLELE1 A1FREQ N TEST BETA SE CHISQ LOG10P EXTRA" > ${REGENIE_FINAL_DIR}/regenie.${PHENOTYPE_ITEM}.summary_results.txt
+
+			# Reset IFS to its original value
+    		IFS=$OLD_IFS
+			for CHR in $(seq 1 22); do
+				# which chromosome are we processing?
+				echo "Processing chromosome ${CHR}..."
+				cat ${STEP2_QT_OUTPUT_DIR}/*.chr${CHR}_${PHENOTYPE_ITEM}.regenie | grep -v "#" | tail -n +2 | awk ' { print $1, $2, $3, $4, $5, $6, $7, $8, $9, $10, $11, $12, $13 } ' >> ${REGENIE_FINAL_DIR}/regenie.${PHENOTYPE_ITEM}.summary_results.txt
+				echo "/////////////////////////////////////////////////////////////////////////////////////////////////////////"
+				echo ""
+			done
+			echo ""
+			gzip -vf ${REGENIE_FINAL_DIR}/regenie.${PHENOTYPE_ITEM}.summary_results.txt
+		done
+		
+	elif [ "${TRAIT_TYPE}" == 'BINARY' ]; then
+		echo "All arguments are passed. These are the settings:"
+		echo "  * SAMPLE FILE: 				${SAMPLE_FILE}"
+		echo "  * QUANTATIVE COVARIATES: 	${COVARIATE_QUANTATIVE}"
+		echo "  * BINARY COVARIATES: 		${COVARIATE_BINARY}"
+		echo "  * QUANTATIVE PHENOTYPE: 	-NOT USED-"
+		echo "  * BINARY PHENOTYPE: 		${PHENOTYPE_BINARY}"
+		echo ""
+		echo "  * BLOCK SIZE: 				${REGENIE_STEP2_BZISE}"
+		echo ""
+		echo ""
+		echo "Start processing REGENIE step 2 for BINARY traits"
+		echo ""
+		
+		IFS=','  # Set comma as the delimiter
+		for PHENOTYPE_ITEM in $PHENOTYPE_BINARY; do
+			echo "Wrapping up for BINARY PHENOTYPE: ${PHENOTYPE_ITEM}"
+			# create results file
+			###      1     2    3   4  5            6            7              8    9      10     11     12     CALC 13 CALC 14 15  16 17 # AUTOSOMAL & X CHROMOSOMES
+			# echo "ALTID RSID CHR BP OtherAlleleA CodedAlleleB AvgMaxPostCall Info all_AA all_AB all_BB TotalN MAC MAF CAF HWE P BETA SE" > ${PHENO_OUTPUT_DIR}/${STUDY_TYPE}.${ANALYSIS_TYPE}.${REFERENCE}.${PHENOTYPE}.${EXCLUSION}.summary_results.txt
+			echo "CHROM GENPOS ID ALLELE0 ALLELE1 A1FREQ N TEST BETA SE CHISQ LOG10P EXTRA" > ${REGENIE_FINAL_DIR}/regenie.${PHENOTYPE_ITEM}.summary_results.txt
+
+			# Reset IFS to its original value
+    		IFS=$OLD_IFS
+			for CHR in $(seq 1 22); do
+				# which chromosome are we processing?
+				echo "Processing chromosome ${CHR}..."
+				cat ${STEP2_BT_OUTPUT_DIR}/*.chr${CHR}_${PHENOTYPE_ITEM}.regenie | grep -v "#" | tail -n +2 | awk ' { print $1, $2, $3, $4, $5, $6, $7, $8, $9, $10, $11, $12, $13 } ' >> ${REGENIE_FINAL_DIR}/regenie.${PHENOTYPE_ITEM}.summary_results.txt
+				echo "/////////////////////////////////////////////////////////////////////////////////////////////////////////"
+				echo ""
+			done
+			echo ""
+			gzip -vf ${REGENIE_FINAL_DIR}/regenie.${PHENOTYPE_ITEM}.summary_results.txt
+		done
+	fi
+
+### END of if-else statement for the number of command-line arguments passed ###
+fi
+
+# script_copyright_message
diff --git a/gwastoolkit.run.sh b/gwastoolkit.run.sh
index fa64708..30ed4d7 100755
--- a/gwastoolkit.run.sh
+++ b/gwastoolkit.run.sh
@@ -95,6 +95,22 @@ script_arguments_error_analysis_type() {
   			exit 1
 }
 
+script_arguments_error_gwas_type() {
+			echo "$1"
+			echo ""
+			echo "      *** ERROR *** ERROR --- $(basename "${0}") --- ERROR *** ERROR ***"
+			echo ""
+			echo " You must supply the correct argument for GWAS:"
+			echo " * [SNPTEST]      -- genome-wide association study of traits in ${PHENOTYPE_FILE} using SNPTEST."
+			echo " * [REGENIE]      -- genome-wide association study of traits in ${PHENOTYPE_FILE} using REGENIE."
+			echo ""
+			echo " Please refer to instruction above."
+			echo ""
+			echo "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
+			# The wrong arguments are passed, so we'll exit the script now!
+  			exit 1
+}
+
 echobold "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
 echobold "                                               GWASTOOLKIT"
 echobold "           individual variant, per-gene, regional, or genome-wide association study of a trait"
@@ -109,6 +125,7 @@ echobold "              - Aisha Gohar (a.gohar@umcutrecht.nl)"
 echobold "              - Jessica van Setten (j.vansetten@umcutrecht.nl)"
 echobold "              - Tim Bezemer (t.bezemer-2@umcutrecht.nl)"
 echobold "              - Lennart P.L. Landsmeer (l.p.l.landsmeer-2@umcutrecht.nl)"
+echobold "              - Tim S. Peters (t.s.peters-4@umcutrecht.nl)"
 echobold ""
 echobold " Description: Perform individual variant, regional or genome-wide association "
 echobold "              analysis on some phenotype(s). It will do the following:"
@@ -217,49 +234,152 @@ else
 	### SUBMIT SNPTEST_PHENO
 
 	if [[ ${ANALYSIS_TYPE} = "GWAS" ]]; then
-		echo "Creating jobs to perform GWAS on your phenotype(s)..."
-    ### Sending analizer.sh to sbatch
-    ${GWASTOOLKITDIR}/gwastoolkit.analyzer.sh ${CONFIGURATIONFILE} ${DATE_TRACK}
-    ### Create QC bash-script to send to qsub
-		for PHENOTYPE in ${PHENOTYPES}; do
+		if [[ ${GWAS_TYPE} = "SNPTEST" ]]; then
+			echo "Creating jobs to perform SNPTEST GWAS on your phenotype(s)..."
+			### Sending analizer.sh to sbatch
+			${GWASTOOLKITDIR}/gwastoolkit.analyzer.sh ${CONFIGURATIONFILE} ${DATE_TRACK}
+			### Create QC bash-script to send to qsub
+			for PHENOTYPE in ${PHENOTYPES}; do
+
+				PHENO_OUTPUT_DIR=${PROJECT}/snptest_results/${PHENOTYPE}
+
+				printf "%s\n" "#!/bin/bash" "#" "${GWASTOOLKITDIR}/gwastoolkit.qc.sh ${CONFIGURATIONFILE} ${PHENOTYPE} " > ${PHENO_OUTPUT_DIR}/qc.${STUDY_TYPE}.${ANALYSIS_TYPE}.${PHENOTYPE}.${EXCLUSION}.sh
+				### Submit QC script
+				### The option '-hold_jid' indicates that the following qsub will not start until all jobs with '-N SOMENAMEFORTHESCRIPT' are finished
+				JOB_ID_QC=$(sbatch --parsable -J QC.${STUDY_TYPE}.${ANALYSIS_TYPE}.${PHENOTYPE}.${EXCLUSION} --depend=afterany:$(squeue --noheader --format %i --name ANALYZER.DONE.${DATE_TRACK}) -o ${PHENO_OUTPUT_DIR}/qc.${STUDY_TYPE}.${ANALYSIS_TYPE}.${PHENOTYPE}.${EXCLUSION}.log -e ${PHENO_OUTPUT_DIR}/qc.${STUDY_TYPE}.${ANALYSIS_TYPE}.${PHENOTYPE}.${EXCLUSION}.errors --mem=${QMEMGWAS} -t ${QTIMEGWAS} --mail-user=${YOUREMAIL} --mail-type=${MAILSETTINGS} -D ${PHENO_OUTPUT_DIR} ${PHENO_OUTPUT_DIR}/qc.${STUDY_TYPE}.${ANALYSIS_TYPE}.${PHENOTYPE}.${EXCLUSION}.sh)
+				echo ""
+
+				### Create plotter bash-script to send to qsub
+				printf "%s\n" "#!/bin/bash" "#" "${GWASTOOLKITDIR}/gwastoolkit.plotter.sh ${CONFIGURATIONFILE} ${PHENOTYPE} " > ${PHENO_OUTPUT_DIR}/plotter.${STUDY_TYPE}.${ANALYSIS_TYPE}.${PHENOTYPE}.${EXCLUSION}.sh
+				### Submit plotter script
+				JOB_ID_PLOTTER=$(sbatch --parsable -J PLOTTER.${STUDY_TYPE}.${ANALYSIS_TYPE}.${PHENOTYPE}.${EXCLUSION} --depend=afterany:$(squeue --noheader --format %i --name ANALYZER.DONE.${DATE_TRACK}) -o ${PHENO_OUTPUT_DIR}/plotter.${STUDY_TYPE}.${ANALYSIS_TYPE}.${PHENOTYPE}.${EXCLUSION}.log -e ${PHENO_OUTPUT_DIR}/plotter.${STUDY_TYPE}.${ANALYSIS_TYPE}.${PHENOTYPE}.${EXCLUSION}.errors --mem=${QMEMGWASPLOT} -t ${QTIMEGWASPLOT} --mail-user=${YOUREMAIL} --mail-type=${MAILSETTINGS} -D ${PHENO_OUTPUT_DIR} ${PHENO_OUTPUT_DIR}/plotter.${STUDY_TYPE}.${ANALYSIS_TYPE}.${PHENOTYPE}.${EXCLUSION}.sh)
+				echo ""
+
+				### Create QC plotter bash-script to send to qsub
+				printf "%s\n" "#!/bin/bash" "#" "${GWASTOOLKITDIR}/gwastoolkit.plotter.qc.sh ${CONFIGURATIONFILE} ${PHENOTYPE} " > ${PHENO_OUTPUT_DIR}/qcplotter.${STUDY_TYPE}.${ANALYSIS_TYPE}.${PHENOTYPE}.${EXCLUSION}.sh
+				### Submit QC plotter script
+				JOB_ID_QCPLOTTER=$(sbatch --parsable -J QCPLOTTER.${STUDY_TYPE}.${ANALYSIS_TYPE}.${PHENOTYPE}.${EXCLUSION} --depend=afterany:${JOB_ID_QC} -o ${PHENO_OUTPUT_DIR}/qcplotter.${STUDY_TYPE}.${ANALYSIS_TYPE}.${PHENOTYPE}.${EXCLUSION}.log -e ${PHENO_OUTPUT_DIR}/qcplotter.${STUDY_TYPE}.${ANALYSIS_TYPE}.${PHENOTYPE}.${EXCLUSION}.errors --mem=${QMEMGWASPLOTQC} -t ${QTIMEGWASPLOTQC} --mail-user=${YOUREMAIL} --mail-type=${MAILSETTINGS} -D ${PHENO_OUTPUT_DIR} ${PHENO_OUTPUT_DIR}/qcplotter.${STUDY_TYPE}.${ANALYSIS_TYPE}.${PHENOTYPE}.${EXCLUSION}.sh)
+				echo ""
+
+				#### Create clumper bash-script to send to qsub
+				printf "%s\n" "#!/bin/bash" "#" "${GWASTOOLKITDIR}/gwastoolkit.clumper.sh ${CONFIGURATIONFILE} ${PHENOTYPE} " > ${PHENO_OUTPUT_DIR}/clumper.${STUDY_TYPE}.${ANALYSIS_TYPE}.${PHENOTYPE}.${EXCLUSION}.sh
+				#### Submit clumper script
+				JOB_ID_CLUMPER=$(sbatch --parsable -J CLUMPER.${STUDY_TYPE}.${ANALYSIS_TYPE}.${PHENOTYPE}.${EXCLUSION} --depend=afterany:${JOB_ID_QC} -o ${PHENO_OUTPUT_DIR}/clumper.${STUDY_TYPE}.${ANALYSIS_TYPE}.${PHENOTYPE}.${EXCLUSION}.log -e ${PHENO_OUTPUT_DIR}/clumper.${STUDY_TYPE}.${ANALYSIS_TYPE}.${PHENOTYPE}.${EXCLUSION}.errors --mem=${QMEMGWASCLUMP} -t ${QTIMEGWASCLUMP} --mail-user=${YOUREMAIL} --mail-type=${MAILSETTINGS} -D ${PHENO_OUTPUT_DIR} ${PHENO_OUTPUT_DIR}/clumper.${STUDY_TYPE}.${ANALYSIS_TYPE}.${PHENOTYPE}.${EXCLUSION}.sh)
+				echo ""
+
+				##### Create locuszoom bash-script to send to qsub
+				printf "%s\n" "#!/bin/bash" "#" "${GWASTOOLKITDIR}/gwastoolkit.locuszoomer.sh ${CONFIGURATIONFILE} ${PHENOTYPE} " > ${PHENO_OUTPUT_DIR}/locuszoom.${STUDY_TYPE}.${ANALYSIS_TYPE}.${PHENOTYPE}.${EXCLUSION}.sh
+				##### Submit locuszoom script
+				JOB_ID_LZ=$(sbatch --parsable -J LZ.${STUDY_TYPE}.${ANALYSIS_TYPE}.${PHENOTYPE}.${EXCLUSION} --depend=afterany:${JOB_ID_CLUMPER} -o ${PHENO_OUTPUT_DIR}/locuszoom.${STUDY_TYPE}.${ANALYSIS_TYPE}.${PHENOTYPE}.${EXCLUSION}.log -e ${PHENO_OUTPUT_DIR}/locuszoom.${STUDY_TYPE}.${ANALYSIS_TYPE}.${PHENOTYPE}.${EXCLUSION}.errors --mem=${QMEMGWASLZOOM} -t ${QTIMEGWASLZOOM} --mail-user=${YOUREMAIL} --mail-type=${MAILSETTINGS} -D ${PHENO_OUTPUT_DIR} ${PHENO_OUTPUT_DIR}/locuszoom.${STUDY_TYPE}.${ANALYSIS_TYPE}.${PHENOTYPE}.${EXCLUSION}.sh)
+
+				##### Create cleaner bash-script to send to qsub
+				printf "%s\n" "#!/bin/bash" "#" "${GWASTOOLKITDIR}/gwastoolkit.cleaner.sh ${CONFIGURATIONFILE} ${PHENOTYPE} " > ${PHENO_OUTPUT_DIR}/cleaner.${STUDY_TYPE}.${ANALYSIS_TYPE}.${PHENOTYPE}.${EXCLUSION}.sh
+				##### Submit cleaner script
+				JOB_ID_CLEANER=$(sbatch --parsable -J CLEANER.${STUDY_TYPE}.${ANALYSIS_TYPE}.${PHENOTYPE}.${EXCLUSION} --depend=afterany:${JOB_ID_LZ} -o ${PHENO_OUTPUT_DIR}/cleaner.${STUDY_TYPE}.${ANALYSIS_TYPE}.${PHENOTYPE}.${EXCLUSION}.log -e ${PHENO_OUTPUT_DIR}/cleaner.${STUDY_TYPE}.${ANALYSIS_TYPE}.${PHENOTYPE}.${EXCLUSION}.errors --mem=${QMEMGWASCLEANER} -t ${QTIMEGWASCLEANER} --mail-user=${YOUREMAIL} --mail-type=${MAILSETTINGS} -D ${PHENO_OUTPUT_DIR} ${PHENO_OUTPUT_DIR}/cleaner.${STUDY_TYPE}.${ANALYSIS_TYPE}.${PHENOTYPE}.${EXCLUSION}.sh)
 
-			PHENO_OUTPUT_DIR=${PROJECT}/snptest_results/${PHENOTYPE}
+			done
 
-			printf "%s\n" "#!/bin/bash" "#" "${GWASTOOLKITDIR}/gwastoolkit.qc.sh ${CONFIGURATIONFILE} ${PHENOTYPE} " > ${PHENO_OUTPUT_DIR}/qc.${STUDY_TYPE}.${ANALYSIS_TYPE}.${PHENOTYPE}.${EXCLUSION}.sh
-			### Submit QC script
-			### The option '-hold_jid' indicates that the following qsub will not start until all jobs with '-N SOMENAMEFORTHESCRIPT' are finished
-			JOB_ID_QC=$(sbatch --parsable -J QC.${STUDY_TYPE}.${ANALYSIS_TYPE}.${PHENOTYPE}.${EXCLUSION} --depend=afterany:$(squeue --noheader --format %i --name ANALYZER.DONE.${DATE_TRACK}) -o ${PHENO_OUTPUT_DIR}/qc.${STUDY_TYPE}.${ANALYSIS_TYPE}.${PHENOTYPE}.${EXCLUSION}.log -e ${PHENO_OUTPUT_DIR}/qc.${STUDY_TYPE}.${ANALYSIS_TYPE}.${PHENOTYPE}.${EXCLUSION}.errors --mem=${QMEMGWAS} -t ${QTIMEGWAS} --mail-user=${YOUREMAIL} --mail-type=${MAILSETTINGS} -D ${PHENO_OUTPUT_DIR} ${PHENO_OUTPUT_DIR}/qc.${STUDY_TYPE}.${ANALYSIS_TYPE}.${PHENOTYPE}.${EXCLUSION}.sh)
-			echo ""
+		elif [[ ${GWAS_TYPE} = "REGENIE" ]]; then
+			echo "Creating jobs to perform REGENIE GWAS on your phenotype(s)..."
 
-			### Create plotter bash-script to send to qsub
-			printf "%s\n" "#!/bin/bash" "#" "${GWASTOOLKITDIR}/gwastoolkit.plotter.sh ${CONFIGURATIONFILE} ${PHENOTYPE} " > ${PHENO_OUTPUT_DIR}/plotter.${STUDY_TYPE}.${ANALYSIS_TYPE}.${PHENOTYPE}.${EXCLUSION}.sh
-			### Submit plotter script
-			JOB_ID_PLOTTER=$(sbatch --parsable -J PLOTTER.${STUDY_TYPE}.${ANALYSIS_TYPE}.${PHENOTYPE}.${EXCLUSION} --depend=afterany:$(squeue --noheader --format %i --name ANALYZER.DONE.${DATE_TRACK}) -o ${PHENO_OUTPUT_DIR}/plotter.${STUDY_TYPE}.${ANALYSIS_TYPE}.${PHENOTYPE}.${EXCLUSION}.log -e ${PHENO_OUTPUT_DIR}/plotter.${STUDY_TYPE}.${ANALYSIS_TYPE}.${PHENOTYPE}.${EXCLUSION}.errors --mem=${QMEMGWASPLOT} -t ${QTIMEGWASPLOT} --mail-user=${YOUREMAIL} --mail-type=${MAILSETTINGS} -D ${PHENO_OUTPUT_DIR} ${PHENO_OUTPUT_DIR}/plotter.${STUDY_TYPE}.${ANALYSIS_TYPE}.${PHENOTYPE}.${EXCLUSION}.sh)
-			echo ""
+			### vcf.gx -> pgen ??
 
-			### Create QC plotter bash-script to send to qsub
-			printf "%s\n" "#!/bin/bash" "#" "${GWASTOOLKITDIR}/gwastoolkit.plotter.qc.sh ${CONFIGURATIONFILE} ${PHENOTYPE} " > ${PHENO_OUTPUT_DIR}/qcplotter.${STUDY_TYPE}.${ANALYSIS_TYPE}.${PHENOTYPE}.${EXCLUSION}.sh
-			### Submit QC plotter script
-			JOB_ID_QCPLOTTER=$(sbatch --parsable -J QCPLOTTER.${STUDY_TYPE}.${ANALYSIS_TYPE}.${PHENOTYPE}.${EXCLUSION} --depend=afterany:${JOB_ID_QC} -o ${PHENO_OUTPUT_DIR}/qcplotter.${STUDY_TYPE}.${ANALYSIS_TYPE}.${PHENOTYPE}.${EXCLUSION}.log -e ${PHENO_OUTPUT_DIR}/qcplotter.${STUDY_TYPE}.${ANALYSIS_TYPE}.${PHENOTYPE}.${EXCLUSION}.errors --mem=${QMEMGWASPLOTQC} -t ${QTIMEGWASPLOTQC} --mail-user=${YOUREMAIL} --mail-type=${MAILSETTINGS} -D ${PHENO_OUTPUT_DIR} ${PHENO_OUTPUT_DIR}/qcplotter.${STUDY_TYPE}.${ANALYSIS_TYPE}.${PHENOTYPE}.${EXCLUSION}.sh)
-			echo ""
+			### merge seperate pgen chromosomes into one
 
-			#### Create clumper bash-script to send to qsub
-			printf "%s\n" "#!/bin/bash" "#" "${GWASTOOLKITDIR}/gwastoolkit.clumper.sh ${CONFIGURATIONFILE} ${PHENOTYPE} " > ${PHENO_OUTPUT_DIR}/clumper.${STUDY_TYPE}.${ANALYSIS_TYPE}.${PHENOTYPE}.${EXCLUSION}.sh
-			#### Submit clumper script
-			JOB_ID_CLUMPER=$(sbatch --parsable -J CLUMPER.${STUDY_TYPE}.${ANALYSIS_TYPE}.${PHENOTYPE}.${EXCLUSION} --depend=afterany:${JOB_ID_QC} -o ${PHENO_OUTPUT_DIR}/clumper.${STUDY_TYPE}.${ANALYSIS_TYPE}.${PHENOTYPE}.${EXCLUSION}.log -e ${PHENO_OUTPUT_DIR}/clumper.${STUDY_TYPE}.${ANALYSIS_TYPE}.${PHENOTYPE}.${EXCLUSION}.errors --mem=${QMEMGWASCLUMP} -t ${QTIMEGWASCLUMP} --mail-user=${YOUREMAIL} --mail-type=${MAILSETTINGS} -D ${PHENO_OUTPUT_DIR} ${PHENO_OUTPUT_DIR}/clumper.${STUDY_TYPE}.${ANALYSIS_TYPE}.${PHENOTYPE}.${EXCLUSION}.sh)
+			### Create QC Pre-processing bash-script to send to sbatch
+			echo "SUBMITTING JOB: Regenie Quality Control (Pre-processing)"
+			printf "%s\n" "#!/bin/bash" "#" "${GWASTOOLKITDIR}/gwastoolkit.regenie.qc.sh ${CONFIGURATIONFILE} " > ${PROJECT}/regenie.qc.${STUDY_TYPE}.${ANALYSIS_TYPE}.sh
+			### Submit QC Pre-processing script
+			### The option '-hold_jid' indicates that the following qsub will not start until all jobs with '-N SOMENAMEFORTHESCRIPT' are finished
+			JOB_ID_QC=$(sbatch --parsable -J REGENIE.QC.${STUDY_TYPE}.${ANALYSIS_TYPE} -o ${PROJECT}/regenie.qc.${STUDY_TYPE}.${ANALYSIS_TYPE}.log -e ${PROJECT}/regenie.qc.${STUDY_TYPE}.${ANALYSIS_TYPE}.errors --mem=${QMEMGWASREGENIE} -t ${QTIMEGWASREGENIE} --mail-user=${YOUREMAIL} --mail-type=${MAILSETTINGS} -D ${PROJECT} ${PROJECT}/regenie.qc.${STUDY_TYPE}.${ANALYSIS_TYPE}.sh)
 			echo ""
 
-			##### Create locuszoom bash-script to send to qsub
-			printf "%s\n" "#!/bin/bash" "#" "${GWASTOOLKITDIR}/gwastoolkit.locuszoomer.sh ${CONFIGURATIONFILE} ${PHENOTYPE} " > ${PHENO_OUTPUT_DIR}/locuszoom.${STUDY_TYPE}.${ANALYSIS_TYPE}.${PHENOTYPE}.${EXCLUSION}.sh
-			##### Submit locuszoom script
-			JOB_ID_LZ=$(sbatch --parsable -J LZ.${STUDY_TYPE}.${ANALYSIS_TYPE}.${PHENOTYPE}.${EXCLUSION} --depend=afterany:${JOB_ID_CLUMPER} -o ${PHENO_OUTPUT_DIR}/locuszoom.${STUDY_TYPE}.${ANALYSIS_TYPE}.${PHENOTYPE}.${EXCLUSION}.log -e ${PHENO_OUTPUT_DIR}/locuszoom.${STUDY_TYPE}.${ANALYSIS_TYPE}.${PHENOTYPE}.${EXCLUSION}.errors --mem=${QMEMGWASLZOOM} -t ${QTIMEGWASLZOOM} --mail-user=${YOUREMAIL} --mail-type=${MAILSETTINGS} -D ${PHENO_OUTPUT_DIR} ${PHENO_OUTPUT_DIR}/locuszoom.${STUDY_TYPE}.${ANALYSIS_TYPE}.${PHENOTYPE}.${EXCLUSION}.sh)
-
-			##### Create cleaner bash-script to send to qsub
-			printf "%s\n" "#!/bin/bash" "#" "${GWASTOOLKITDIR}/gwastoolkit.cleaner.sh ${CONFIGURATIONFILE} ${PHENOTYPE} " > ${PHENO_OUTPUT_DIR}/cleaner.${STUDY_TYPE}.${ANALYSIS_TYPE}.${PHENOTYPE}.${EXCLUSION}.sh
-			##### Submit cleaner script
- 			JOB_ID_CLEANER=$(sbatch --parsable -J CLEANER.${STUDY_TYPE}.${ANALYSIS_TYPE}.${PHENOTYPE}.${EXCLUSION} --depend=afterany:${JOB_ID_LZ} -o ${PHENO_OUTPUT_DIR}/cleaner.${STUDY_TYPE}.${ANALYSIS_TYPE}.${PHENOTYPE}.${EXCLUSION}.log -e ${PHENO_OUTPUT_DIR}/cleaner.${STUDY_TYPE}.${ANALYSIS_TYPE}.${PHENOTYPE}.${EXCLUSION}.errors --mem=${QMEMGWASCLEANER} -t ${QTIMEGWASCLEANER} --mail-user=${YOUREMAIL} --mail-type=${MAILSETTINGS} -D ${PHENO_OUTPUT_DIR} ${PHENO_OUTPUT_DIR}/cleaner.${STUDY_TYPE}.${ANALYSIS_TYPE}.${PHENOTYPE}.${EXCLUSION}.sh)
+			##### Running REGENIE for BINARY Traits
+			if [ -n "$PHENOTYPE_BINARY" ]; then
+				echo "*** BINARY Phenotypes found ***"
+				echo "-	SUBMITTING JOB: Regenie Step 1"
+				##### Regenie step 1
+				printf "%s\n" "#!/bin/bash" "#" "${GWASTOOLKITDIR}/gwastoolkit.regenie.step1.sh ${CONFIGURATIONFILE} BINARY " > ${PROJECT}/regenie.BT.step1.${STUDY_TYPE}.${ANALYSIS_TYPE}.sh
+				### Submit QC Pre-processing script
+				### The option '-hold_jid' indicates that the following qsub will not start until all jobs with '-N SOMENAMEFORTHESCRIPT' are finished
+				JOB_ID_REGENIE_BT_STEP1=$(sbatch --parsable -J REGENIE.BT.STEP1.${STUDY_TYPE}.${ANALYSIS_TYPE} --depend=afterany:${JOB_ID_QC} -o ${PROJECT}/regenie.BT.step1.${STUDY_TYPE}.${ANALYSIS_TYPE}.log -e ${PROJECT}/regenie.BT.step1.${STUDY_TYPE}.${ANALYSIS_TYPE}.errors --mem=${QMEMGWASREGENIE1} -t ${QTIMEGWASREGENIE1} -c 8 --mail-user=${YOUREMAIL} --mail-type=${MAILSETTINGS} -D ${PROJECT} ${PROJECT}/regenie.BT.step1.${STUDY_TYPE}.${ANALYSIS_TYPE}.sh)
+				
+				# DEBUG
+				# JOB_ID_REGENIE_BT_STEP1=$(sbatch --parsable -J REGENIE.BT.STEP1.${STUDY_TYPE}.${ANALYSIS_TYPE} -o ${PROJECT}/regenie.BT.step1.${STUDY_TYPE}.${ANALYSIS_TYPE}.log -e ${PROJECT}/regenie.BT.step1.${STUDY_TYPE}.${ANALYSIS_TYPE}.errors --mem=${QMEMGWASREGENIE1} -t ${QTIMEGWASREGENIE1} -c 8 --mail-user=${YOUREMAIL} --mail-type=${MAILSETTINGS} -D ${PROJECT} ${PROJECT}/regenie.BT.step1.${STUDY_TYPE}.${ANALYSIS_TYPE}.sh)
+				echo ""
+
+				echo "-	SUBMITTING JOB: Regenie Step 2"
+				##### Regenie step 2 
+				printf "%s\n" "#!/bin/bash" "#" "${GWASTOOLKITDIR}/gwastoolkit.regenie.step2.sh ${CONFIGURATIONFILE} BINARY " > ${PROJECT}/regenie.BT.step2.${STUDY_TYPE}.${ANALYSIS_TYPE}.sh
+				### Submit QC Pre-processing script
+				### The option '-hold_jid' indicates that the following qsub will not start until all jobs with '-N SOMENAMEFORTHESCRIPT' are finished
+				JOB_ID_REGENIE_BT_STEP2=$(sbatch --parsable -J REGENIE.BT.STEP2.${STUDY_TYPE}.${ANALYSIS_TYPE} --depend=afterany:${JOB_ID_REGENIE_BT_STEP1} -o ${PROJECT}/regenie.BT.step2.${STUDY_TYPE}.${ANALYSIS_TYPE}.log -e ${PROJECT}/regenie.BT.step2.${STUDY_TYPE}.${ANALYSIS_TYPE}.errors --mem=${QMEMGWASREGENIE2} -t ${QTIMEGWASREGENIE2} -c 8 --mail-user=${YOUREMAIL} --mail-type=${MAILSETTINGS} -D ${PROJECT} ${PROJECT}/regenie.BT.step2.${STUDY_TYPE}.${ANALYSIS_TYPE}.sh)
+				
+				# DEBUG
+				# JOB_ID_REGENIE_BT_STEP2=$(sbatch --parsable -J REGENIE.BT.STEP2.${STUDY_TYPE}.${ANALYSIS_TYPE} -o ${PROJECT}/regenie.BT.step2.${STUDY_TYPE}.${ANALYSIS_TYPE}.log -e ${PROJECT}/regenie.BT.step2.${STUDY_TYPE}.${ANALYSIS_TYPE}.errors --mem=${QMEMGWASREGENIE2} -t ${QTIMEGWASREGENIE2} -c 8 --mail-user=${YOUREMAIL} --mail-type=${MAILSETTINGS} -D ${PROJECT} ${PROJECT}/regenie.BT.step2.${STUDY_TYPE}.${ANALYSIS_TYPE}.sh)
+				echo ""
+
+				echo "-	SUBMITTING JOB: Regenie Wrapper"
+				##### Regenie wrapup
+				printf "%s\n" "#!/bin/bash" "#" "${GWASTOOLKITDIR}/gwastoolkit.regenie.wrapper.sh ${CONFIGURATIONFILE} BINARY " > ${PROJECT}/regenie.BT.wrapper.${STUDY_TYPE}.${ANALYSIS_TYPE}.sh
+				### Submit QC Pre-processing script
+				### The option '-hold_jid' indicates that the following qsub will not start until all jobs with '-N SOMENAMEFORTHESCRIPT' are finished
+				JOB_ID_REGENIE_BT_WRAPPER=$(sbatch --parsable -J REGENIE.BT.wrapper.${STUDY_TYPE}.${ANALYSIS_TYPE} --depend=afterany:${JOB_ID_REGENIE_BT_STEP2} -o ${PROJECT}/regenie.BT.wrapper.${STUDY_TYPE}.${ANALYSIS_TYPE}.log -e ${PROJECT}/regenie.BT.wrapper.${STUDY_TYPE}.${ANALYSIS_TYPE}.errors --mem=${QMEMGWASREGENIEWRAP} -t ${QTIMEGWASREGENIEWRAP} -c 8 --mail-user=${YOUREMAIL} --mail-type=${MAILSETTINGS} -D ${PROJECT} ${PROJECT}/regenie.BT.wrapper.${STUDY_TYPE}.${ANALYSIS_TYPE}.sh)
+				
+				# DEBUG
+				# JOB_ID_REGENIE_BT_WRAPPER=$(sbatch --parsable -J REGENIE.BT.wrapper.${STUDY_TYPE}.${ANALYSIS_TYPE} -o ${PROJECT}/regenie.BT.wrapper.${STUDY_TYPE}.${ANALYSIS_TYPE}.log -e ${PROJECT}/regenie.BT.wrapper.${STUDY_TYPE}.${ANALYSIS_TYPE}.errors --mem=${QMEMGWASREGENIEWRAP} -t ${QTIMEGWASREGENIEWRAP} -c 8 --mail-user=${YOUREMAIL} --mail-type=${MAILSETTINGS} -D ${PROJECT} ${PROJECT}/regenie.BT.wrapper.${STUDY_TYPE}.${ANALYSIS_TYPE}.sh)
+				echo ""
+				echo ""
+			else
+				echo "*** No BINARY Phenotypes give ***"
+				echo ""
+			fi
+			
+			##### Running REGENIE for QUANTATIVE Traits
+			if [ -n "$PHENOTYPE_QUANTATIVE" ]; then
+				echo "*** QUANTATIVE Phenotypes found ***"
+				echo "-	SUBMITTING JOB: Regenie Step 1"
+				##### Regenie step 1
+				printf "%s\n" "#!/bin/bash" "#" "${GWASTOOLKITDIR}/gwastoolkit.regenie.step1.sh ${CONFIGURATIONFILE} QUANTATIVE " > ${PROJECT}/regenie.QT.step1.${STUDY_TYPE}.${ANALYSIS_TYPE}.sh
+				### Submit QC Pre-processing script
+				### The option '-hold_jid' indicates that the following qsub will not start until all jobs with '-N SOMENAMEFORTHESCRIPT' are finished
+				JOB_ID_REGENIE_QT_STEP1=$(sbatch --parsable -J REGENIE.QT.STEP1.${STUDY_TYPE}.${ANALYSIS_TYPE} --depend=afterany:${JOB_ID_QC} -o ${PROJECT}/regenie.QT.step1.${STUDY_TYPE}.${ANALYSIS_TYPE}.log -e ${PROJECT}/regenie.QT.step1.${STUDY_TYPE}.${ANALYSIS_TYPE}.errors --mem=${QMEMGWASREGENIE1} -t ${QTIMEGWASREGENIE1} -c 8 --mail-user=${YOUREMAIL} --mail-type=${MAILSETTINGS} -D ${PROJECT} ${PROJECT}/regenie.QT.step1.${STUDY_TYPE}.${ANALYSIS_TYPE}.sh)
+				
+				# DEBUG
+				# JOB_ID_REGENIE_QT_STEP1=$(sbatch --parsable -J REGENIE.QT.STEP1.${STUDY_TYPE}.${ANALYSIS_TYPE} -o ${PROJECT}/regenie.QT.step1.${STUDY_TYPE}.${ANALYSIS_TYPE}.log -e ${PROJECT}/regenie.QT.step1.${STUDY_TYPE}.${ANALYSIS_TYPE}.errors --mem=${QMEMGWASREGENIE1} -t ${QTIMEGWASREGENIE1} -c 8 --mail-user=${YOUREMAIL} --mail-type=${MAILSETTINGS} -D ${PROJECT} ${PROJECT}/regenie.QT.step1.${STUDY_TYPE}.${ANALYSIS_TYPE}.sh)
+				echo ""
+
+				echo "-	SUBMITTING JOB: Regenie Step 2"
+				##### Regenie step 2
+				printf "%s\n" "#!/bin/bash" "#" "${GWASTOOLKITDIR}/gwastoolkit.regenie.step2.sh ${CONFIGURATIONFILE} QUANTATIVE " > ${PROJECT}/regenie.QT.step2.${STUDY_TYPE}.${ANALYSIS_TYPE}.sh
+				### Submit QC Pre-processing script
+				### The option '-hold_jid' indicates that the following qsub will not start until all jobs with '-N SOMENAMEFORTHESCRIPT' are finished
+				JOB_ID_REGENIE_QT_STEP2=$(sbatch --parsable -J REGENIE.QT.STEP2.${STUDY_TYPE}.${ANALYSIS_TYPE} --depend=afterany:${JOB_ID_REGENIE_QT_STEP1} -o ${PROJECT}/regenie.QT.step2.${STUDY_TYPE}.${ANALYSIS_TYPE}.log -e ${PROJECT}/regenie.QT.step2.${STUDY_TYPE}.${ANALYSIS_TYPE}.errors --mem=${QMEMGWASREGENIE2} -t ${QTIMEGWASREGENIE2} -c 8 --mail-user=${YOUREMAIL} --mail-type=${MAILSETTINGS} -D ${PROJECT} ${PROJECT}/regenie.QT.step2.${STUDY_TYPE}.${ANALYSIS_TYPE}.sh)
+				
+				# DEBUG
+				# JOB_ID_REGENIE_QT_STEP2=$(sbatch --parsable -J REGENIE.QT.STEP2.${STUDY_TYPE}.${ANALYSIS_TYPE} -o ${PROJECT}/regenie.QT.step2.${STUDY_TYPE}.${ANALYSIS_TYPE}.log -e ${PROJECT}/regenie.QT.step2.${STUDY_TYPE}.${ANALYSIS_TYPE}.errors --mem=${QMEMGWASREGENIE2} -t ${QTIMEGWASREGENIE2} -c 8 --mail-user=${YOUREMAIL} --mail-type=${MAILSETTINGS} -D ${PROJECT} ${PROJECT}/regenie.QT.step2.${STUDY_TYPE}.${ANALYSIS_TYPE}.sh)
+				echo ""
+
+				echo "-	SUBMITTING JOB: Regenie Wrapper"
+				##### Regenie wrapup
+				printf "%s\n" "#!/bin/bash" "#" "${GWASTOOLKITDIR}/gwastoolkit.regenie.wrapper.sh ${CONFIGURATIONFILE} QUANTATIVE " > ${PROJECT}/regenie.QT.wrapper.${STUDY_TYPE}.${ANALYSIS_TYPE}.sh
+				### Submit QC Pre-processing script
+				### The option '-hold_jid' indicates that the following qsub will not start until all jobs with '-N SOMENAMEFORTHESCRIPT' are finished
+				JOB_ID_REGENIE_QT_WRAPPER=$(sbatch --parsable -J REGENIE.QT.wrapper.${STUDY_TYPE}.${ANALYSIS_TYPE} --depend=afterany:${JOB_ID_REGENIE_QT_STEP2} -o ${PROJECT}/regenie.QT.wrapper.${STUDY_TYPE}.${ANALYSIS_TYPE}.log -e ${PROJECT}/regenie.QT.wrapper.${STUDY_TYPE}.${ANALYSIS_TYPE}.errors --mem=${QMEMGWASREGENIEWRAP} -t ${QTIMEGWASREGENIEWRAP} -c 8 --mail-user=${YOUREMAIL} --mail-type=${MAILSETTINGS} -D ${PROJECT} ${PROJECT}/regenie.QT.wrapper.${STUDY_TYPE}.${ANALYSIS_TYPE}.sh)
+				
+				# DEBUG
+				# JOB_ID_REGENIE_QT_WRAPPER=$(sbatch --parsable -J REGENIE.QT.wrapper.${STUDY_TYPE}.${ANALYSIS_TYPE} -o ${PROJECT}/regenie.QT.wrapper.${STUDY_TYPE}.${ANALYSIS_TYPE}.log -e ${PROJECT}/regenie.QT.wrapper.${STUDY_TYPE}.${ANALYSIS_TYPE}.errors --mem=${QMEMGWASREGENIEWRAP} -t ${QTIMEGWASREGENIEWRAP} -c 8 --mail-user=${YOUREMAIL} --mail-type=${MAILSETTINGS} -D ${PROJECT} ${PROJECT}/regenie.QT.wrapper.${STUDY_TYPE}.${ANALYSIS_TYPE}.sh)
+				echo ""
+				echo ""
+			else
+				echo "No QUANTATIVE Phenotypes give"
+				echo ""
+			fi
+		else
+			### If arguments are not met then this error message will be displayed
+			script_arguments_error_gwas_type
 
-		done
+		fi
 
 	elif [[ ${ANALYSIS_TYPE} = "VARIANT" ]]; then