diff --git a/Makefile_deprecated b/Makefile_deprecated
deleted file mode 100644
index df9617ce9..000000000
--- a/Makefile_deprecated
+++ /dev/null
@@ -1,186 +0,0 @@
-PROJECT_ID ?= open-targets-genetics-dev
-REGION ?= europe-west1
-CLUSTER_NAME ?= ${USER}-genetics-etl
-PROJECT_NUMBER ?= $$(gcloud projects list --filter=${PROJECT_ID} --format="value(PROJECT_NUMBER)")
-APP_NAME ?= $$(cat pyproject.toml| grep name | cut -d" " -f3 | sed  's/"//g')
-VERSION_NO ?= $$(poetry version --short)
-SRC_WITH_DEPS ?= code_bundle
-
-.PHONY: $(shell sed -n -e '/^$$/ { n ; /^[^ .\#][^ ]*:/ { s/:.*$$// ; p ; } ; }' $(MAKEFILE_LIST))
-
-.DEFAULT_GOAL := help
-
-help: ## This is help
-	@awk 'BEGIN {FS = ":.*?## "} /^[a-zA-Z_-]+:.*?## / {printf "\033[36m%-30s\033[0m %s\n", $$1, $$2}' $(MAKEFILE_LIST)
-
-clean: ## CleanUp Prior to Build
-	@rm -Rf ./dist
-	@rm -Rf ./${SRC_WITH_DEPS}
-	@rm -f requirements.txt
-
-setup-dev: SHELL:=/bin/bash
-setup-dev: ## Setup dev environment
-	@. utils/install_dependencies.sh
-
-build: clean ## Build Python Package with Dependencies
-	@echo "Packaging Code and Dependencies for ${APP_NAME}-${VERSION_NO}"
-	@rm -rf ./dist
-	@poetry build
-	@cp ./src/*.py ./dist
-	@poetry run python ./utils/configure.py --cfg job > ./dist/config.yaml
-	@echo "Uploading to Dataproc"
-	@gsutil cp ./dist/${APP_NAME}-${VERSION_NO}-py3-none-any.whl gs://genetics_etl_python_playground/initialisation/
-	@gsutil cp ./utils/initialise_cluster.sh gs://genetics_etl_python_playground/initialisation/
-
-prepare_pics:  ## Create cluster for variant annotation:
-	gcloud dataproc clusters create ${CLUSTER_NAME} \
-        --image-version=2.0 \
-        --project=${PROJECT_ID} \
-        --region=${REGION} \
-		--master-machine-type=n1-highmem-96 \
-        --enable-component-gateway \
-		--num-master-local-ssds=1 \
-		--master-local-ssd-interface=NVME \
-        --metadata="PACKAGE=gs://genetics_etl_python_playground/initialisation/${APP_NAME}-${VERSION_NO}-py3-none-any.whl" \
-        --initialization-actions=gs://genetics_etl_python_playground/initialisation/initialise_cluster.sh \
-        --single-node \
-		--max-idle=10m
-
-prepare_variant_annotation:  ## Create cluster for variant annotation
-	gcloud dataproc clusters create ${CLUSTER_NAME} \
-        --image-version=2.0 \
-        --project=${PROJECT_ID} \
-        --region=${REGION} \
-		--master-machine-type=n1-highmem-96 \
-        --enable-component-gateway \
-        --metadata="PACKAGE=gs://genetics_etl_python_playground/initialisation/${APP_NAME}-${VERSION_NO}-py3-none-any.whl" \
-        --initialization-actions=gs://genetics_etl_python_playground/initialisation/initialise_cluster.sh \
-        --single-node \
-        --max-idle=10m
-
-prepare_variant_index: ## Create cluster for variant index generation
-	gcloud dataproc clusters create ${CLUSTER_NAME} \
-		--image-version=2.0 \
-		--project=${PROJECT_ID} \
-		--region=${REGION} \
-		--master-machine-type=n1-highmem-32 \
-		--metadata="PACKAGE=gs://genetics_etl_python_playground/initialisation/${APP_NAME}-${VERSION_NO}-py3-none-any.whl" \
-		--initialization-actions=gs://genetics_etl_python_playground/initialisation/initialise_cluster.sh \
-		--enable-component-gateway \
-		--single-node \
-		--max-idle=10m
-
-prepare_v2g: ## Create cluster for variant to gene data generation
-	gcloud dataproc clusters create ${CLUSTER_NAME} \
-		--image-version=2.0 \
-		--project=${PROJECT_ID} \
-		--region=${REGION} \
-		--master-machine-type=n1-highmem-64 \
-		--enable-component-gateway \
-		--metadata="PACKAGE=gs://genetics_etl_python_playground/initialisation/${APP_NAME}-${VERSION_NO}-py3-none-any.whl" \
-		--initialization-actions=gs://genetics_etl_python_playground/initialisation/initialise_cluster.sh \
-		--single-node \
-		--max-idle=10m
-
-prepare_v2g: ## Create cluster for variant to gene data generation
-	gcloud dataproc clusters create ${CLUSTER_NAME} \
-		--image-version=2.0 \
-		--project=${PROJECT_ID} \
-		--region=${REGION} \
-		--master-machine-type=n1-highmem-64 \
-		--enable-component-gateway \
-		--metadata="PACKAGE=gs://genetics_etl_python_playground/initialisation/${APP_NAME}-${VERSION_NO}-py3-none-any.whl" \
-		--initialization-actions=gs://genetics_etl_python_playground/initialisation/initialise_cluster.sh \
-		--single-node \
-		--max-idle=10m
-
-prepare_coloc: ## Create cluster for coloc
-	gcloud dataproc clusters create ${CLUSTER_NAME} \
-		--image-version=2.0 \
-		--project=${PROJECT_ID} \
-		--region=${REGION} \
-		--master-machine-type=n1-highmem-64 \
-		--num-master-local-ssds=1 \
-		--master-local-ssd-interface=NVME \
-		--enable-component-gateway \
-		--metadata="PACKAGE=gs://genetics_etl_python_playground/initialisation/${APP_NAME}-${VERSION_NO}-py3-none-any.whl" \
-		--initialization-actions=gs://genetics_etl_python_playground/initialisation/initialise_cluster.sh \
-		--single-node \
-		--max-idle=10m
-
-prepare_gwas: ## Create cluster for gwas data generation
-	gcloud dataproc clusters create ${CLUSTER_NAME} \
-		--image-version=2.0 \
-		--project=${PROJECT_ID} \
-		--region=${REGION} \
-		--master-machine-type=n1-highmem-32 \
-		--metadata="PACKAGE=gs://genetics_etl_python_playground/initialisation/${APP_NAME}-${VERSION_NO}-py3-none-any.whl" \
-		--initialization-actions=gs://genetics_etl_python_playground/initialisation/initialise_cluster.sh \
-		--enable-component-gateway \
-		--single-node \
-		--max-idle=10m
-
-run_coloc: ## Generate coloc results
-	gcloud dataproc jobs submit pyspark ./dist/run_coloc.py \
-    --cluster=${CLUSTER_NAME} \
-    --files=./dist/config.yaml \
-    --py-files=gs://genetics_etl_python_playground/initialisation/${APP_NAME}-${VERSION_NO}-py3-none-any.whl \
-    --project=${PROJECT_ID} \
-    --region=${REGION}
-
-run_v2g: ## Generate V2G dataset
-	gcloud dataproc jobs submit pyspark ./dist/run_v2g.py \
-	--cluster=${CLUSTER_NAME} \
-    --files=./dist/config.yaml \
-    --py-files=gs://genetics_etl_python_playground/initialisation/${APP_NAME}-${VERSION_NO}-py3-none-any.whl \
-    --project=${PROJECT_ID} \
-    --region=${REGION}
-
-run_v2g: ## Generate V2G dataset
-	gcloud dataproc jobs submit pyspark ./dist/run_v2g.py \
-	--cluster=${CLUSTER_NAME} \
-    --files=./dist/config.yaml \
-    --py-files=gs://genetics_etl_python_playground/initialisation/${APP_NAME}-${VERSION_NO}-py3-none-any.whl \
-    --project=${PROJECT_ID} \
-    --region=${REGION}
-
-run_variant_annotation: ## Generate variant annotation dataset
-	gcloud dataproc jobs submit pyspark ./dist/run_variant_annotation.py \
-    --cluster=${CLUSTER_NAME} \
-    --files=./dist/config.yaml \
-	--properties='spark.jars=/opt/conda/miniconda3/lib/python3.8/site-packages/hail/backend/hail-all-spark.jar,spark.driver.extraClassPath=/opt/conda/miniconda3/lib/python3.8/site-packages/hail/backend/hail-all-spark.jar,spark.executor.extraClassPath=./hail-all-spark.jar,spark.serializer=org.apache.spark.serializer.KryoSerializer,spark.kryo.registrator=is.hail.kryo.HailKryoRegistrator' \
-	--project=${PROJECT_ID} \
-    --region=${REGION}
-
-run_variant_index: ## Generate variant index dataset
-	gcloud dataproc jobs submit pyspark ./dist/run_variant_index.py \
-	--cluster=${CLUSTER_NAME} \
-    --files=./dist/config.yaml \
-    --py-files=gs://genetics_etl_python_playground/initialisation/${APP_NAME}-${VERSION_NO}-py3-none-any.whl \
-    --project=${PROJECT_ID} \
-    --region=${REGION}
-
-run_gwas: ## Ingest gwas dataset on a dataproc cluster
-	gcloud dataproc jobs submit pyspark ./dist/run_gwas_ingest.py \
-	--cluster=${CLUSTER_NAME} \
-    --files=./dist/config.yaml \
-	--properties='spark.jars=/opt/conda/miniconda3/lib/python3.8/site-packages/hail/backend/hail-all-spark.jar,spark.driver.extraClassPath=/opt/conda/miniconda3/lib/python3.8/site-packages/hail/backend/hail-all-spark.jar,spark.executor.extraClassPath=./hail-all-spark.jar,spark.serializer=org.apache.spark.serializer.KryoSerializer,spark.kryo.registrator=is.hail.kryo.HailKryoRegistrator' \
-    --py-files=gs://genetics_etl_python_playground/initialisation/${APP_NAME}-${VERSION_NO}-py3-none-any.whl \
-    --project=${PROJECT_ID} \
-    --region=${REGION}
-
-run_pics: ## Run pics method
-	gcloud dataproc jobs submit pyspark ./dist/pics_experiment.py \
-    --cluster=${CLUSTER_NAME} \
-    --files=./dist/config.yaml \
-	--properties='spark.jars=/opt/conda/miniconda3/lib/python3.8/site-packages/hail/backend/hail-all-spark.jar,spark.driver.extraClassPath=/opt/conda/miniconda3/lib/python3.8/site-packages/hail/backend/hail-all-spark.jar,spark.executor.extraClassPath=./hail-all-spark.jar,spark.serializer=org.apache.spark.serializer.KryoSerializer,spark.kryo.registrator=is.hail.kryo.HailKryoRegistrator' \
-	--project=${PROJECT_ID} \
-    --region=${REGION}
-
-run_precompute_ld_index: ## Precompute ld-index information
-	gcloud dataproc jobs submit pyspark ./dist/run_precompute_ld_indexes.py \
-    --cluster=${CLUSTER_NAME} \
-    --files=./dist/config.yaml \
-	--properties='spark.jars=/opt/conda/miniconda3/lib/python3.8/site-packages/hail/backend/hail-all-spark.jar,spark.driver.extraClassPath=/opt/conda/miniconda3/lib/python3.8/site-packages/hail/backend/hail-all-spark.jar,spark.executor.extraClassPath=./hail-all-spark.jar,spark.serializer=org.apache.spark.serializer.KryoSerializer,spark.kryo.registrator=is.hail.kryo.HailKryoRegistrator' \
-	--project=${PROJECT_ID} \
-    --region=${REGION}