├── CONTRIBUTING.md ├── LICENSE ├── README.md ├── batch ├── README.md ├── build_annotator │ ├── Dockerfile.dbNSFP │ ├── Dockerfile.vep │ ├── README.md │ ├── build_databases.sh │ ├── dbNSFP_container.yaml │ ├── download_dbNSFP.sh │ └── vep_container.yaml ├── run_annotator │ ├── README.md │ ├── run_vep_remote.sh │ ├── vep_into_bigquery_for_docker.sh │ └── vep_schema.json └── vep │ ├── Dockerfile │ ├── README.md │ ├── build_vep_cache.sh │ ├── run_script_with_watchdog.sh │ ├── run_vep.sh │ └── sample_pipeline.yaml ├── curation ├── README.md ├── allPossibleSNPs │ ├── ESP_AA.sql │ ├── ESP_EA.sql │ ├── README.md │ ├── all_possible_snps.sql │ ├── check_joined_annotations.sql │ ├── clinvar.sql │ ├── dbSNP.sql │ ├── fasta_to_kv.py │ ├── join_annotations.sql │ ├── render_templated_sql.py │ └── thousandGenomes.sql └── tables │ ├── AddBigQueryDescriptions.md │ ├── Dockerfile │ ├── README.md │ ├── import_vcf_to_bigquery.py │ ├── launch_import_vcf_to_bigquery.sh │ ├── schema_update_utils.py │ ├── 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