├── .gitignore ├── .idea └── inspectionProfiles │ ├── Project_Default.xml │ └── README.md ├── .pylintrc ├── CONTRIBUTING.md ├── LICENSE ├── README.md ├── cloudbuild.yaml ├── cloudbuild_CI.yaml ├── cloudbuild_release.yaml ├── deploy_and_run_tests.sh ├── docker ├── Dockerfile ├── Dockerfile.custom_dataflow_container └── pipelines_runner.sh ├── docs ├── Variant_Transforms_and_BigQuery.pdf ├── advanced_flags.md ├── bigquery_to_vcf.md ├── data_append.md ├── design_docs.md ├── development_guide.md ├── flattening_table.md ├── images │ ├── CSQ_schema.png │ ├── bigquery_dataset_region.png │ ├── console_quotas.png │ ├── flatten_call_flatten_genotype.png │ ├── flatten_call_flatten_genotype_flatten_alt.png │ ├── flatten_call_flatten_genotype_only_alt.png │ ├── flatten_call_flatten_genotype_orig_alt.png │ ├── flatten_call_names.png │ ├── flatten_call_orig_genotype.png │ ├── flatten_original_full_example.png │ ├── flatten_original_row.png │ ├── flattened_full_example.png │ ├── gnomAD_GO_0006302.png │ ├── gnomAD_HBB_query.png │ ├── query_cost_partitioned_table.svg │ ├── query_cost_unpartitioned_table.svg │ ├── sample_info_table.png │ ├── sharding_per_chromosome.svg │ ├── vcf_to_bq_dataflow_pipeline.png │ ├── vcf_to_bq_load_avro.png │ └── vcf_to_bq_stages.svg ├── large_inputs.md ├── malformed_files.md ├── multiple_files.md ├── query_cost.md ├── release.md ├── sample_queries │ ├── README.md │ └── gnomad │ │ └── gnomad.ipynb ├── setting_region.md ├── sharding.md ├── troubleshooting.md ├── variant_annotation.md ├── variant_merging.md ├── vcf_files_preprocessor.md └── vcf_to_bigquery.md ├── gcp_variant_transforms ├── __init__.py ├── beam_io │ ├── __init__.py │ ├── bgzf.py │ ├── bgzf_io.py │ ├── bgzf_io_test.py │ ├── bgzf_test.py │ ├── vcf_estimate_io.py │ ├── vcf_estimate_io_test.py │ ├── vcf_header_io.py │ ├── vcf_header_io_test.py │ ├── vcf_parser.py │ ├── vcf_parser_test.py │ ├── vcfio.py │ └── vcfio_test.py ├── bq_to_vcf.py ├── bq_to_vcf_test.py ├── data │ ├── schema │ │ └── sample_info.json │ └── sharding_configs │ │ ├── homo_sapiens_default.yaml │ │ └── homo_sapiens_fixed_partitions.yaml ├── libs │ ├── __init__.py │ ├── annotation │ │ ├── README.md │ │ ├── __init__.py │ │ ├── annotation_parser.py │ │ ├── annotation_parser_test.py │ │ └── vep │ │ │ ├── __init__.py │ │ │ ├── descriptions.py │ │ │ ├── file_metadata_stub.py │ │ │ ├── vep_runner.py │ │ │ ├── vep_runner_test.py │ │ │ ├── vep_runner_util.py │ │ │ └── vep_runner_util_test.py │ ├── avro_util.py │ ├── bigquery_row_generator.py │ ├── bigquery_row_generator_test.py │ ├── bigquery_sanitizer.py │ ├── bigquery_sanitizer_test.py │ ├── bigquery_schema_descriptor.py │ ├── bigquery_schema_descriptor_test.py │ ├── bigquery_util.py │ ├── bigquery_util_test.py │ ├── bigquery_vcf_data_converter.py │ ├── bigquery_vcf_data_converter_test.py │ ├── genomic_region_parser.py │ ├── genomic_region_parser_test.py │ ├── hashing_util.py │ ├── hashing_util_test.py │ ├── header_merger.py │ ├── header_merger_test.py │ ├── infer_headers_util.py │ ├── infer_headers_util_test.py │ ├── metrics_util.py │ ├── metrics_util_test.py │ ├── partitioning.py │ ├── partitioning_test.py │ ├── preprocess_reporter.py │ ├── preprocess_reporter_test.py │ ├── processed_variant.py │ ├── processed_variant_test.py │ ├── sample_info_table_schema_generator.py │ ├── sample_info_table_schema_generator_test.py │ ├── schema_converter.py │ ├── schema_converter_test.py │ ├── variant_merge │ │ ├── __init__.py │ │ ├── merge_with_non_variants_strategy.py │ │ ├── merge_with_non_variants_strategy_test.py │ │ ├── move_to_calls_strategy.py │ │ ├── move_to_calls_strategy_test.py │ │ └── variant_merge_strategy.py │ ├── variant_sharding.py │ ├── variant_sharding_test.py │ ├── vcf_field_conflict_resolver.py │ ├── vcf_field_conflict_resolver_test.py │ ├── vcf_file_composer.py │ ├── vcf_header_definitions_merger.py │ ├── vcf_header_definitions_merger_test.py │ ├── vcf_header_parser.py │ ├── vcf_header_parser_test.py │ └── vcf_reserved_fields.py ├── options │ ├── __init__.py │ ├── variant_transform_options.py │ └── variant_transform_options_test.py ├── pipeline_common.py ├── pipeline_common_test.py ├── testing │ ├── __init__.py │ ├── asserts.py │ ├── bigquery_schema_util.py │ ├── data │ │ ├── input_files │ │ │ ├── combine_input │ │ │ └── error_input │ │ ├── schema │ │ │ └── flatten_merge_option_move_to_calls.json │ │ ├── sharding_configs │ │ │ ├── README.md │ │ │ ├── integration_with_residual.yaml │ │ │ ├── integration_without_residual.yaml │ │ │ ├── residual_at_end.yaml │ │ │ ├── residual_in_middle.yaml │ │ │ └── residual_missing.yaml │ │ └── vcf │ │ │ ├── README.md │ │ │ ├── Y.vcf.bgz │ │ │ ├── Y.vcf.bgz.tbi │ │ │ ├── bq_to_vcf │ │ │ └── expected_output │ │ │ │ ├── no_options.vcf │ │ │ │ ├── option_allow_incompatible_schema.vcf │ │ │ │ ├── option_customized_export.vcf │ │ │ │ ├── option_preserve_sample_order.vcf │ │ │ │ ├── option_representative_header_file.vcf │ │ │ │ └── option_use_1_based_coordinate.vcf │ │ │ ├── empty.vcf.gz │ │ │ ├── empty.vcf.gz.tbi │ │ │ ├── incompatible-field-value.vcf │ │ │ ├── infer-header-fields.vcf │ │ │ ├── invalid-4.0-AF-field-removed.vcf │ │ │ ├── invalid-4.0-POS-empty.vcf │ │ │ ├── invalid-4.2-AF-mismatch.vcf │ │ │ ├── merge │ │ │ ├── merge1.vcf │ │ │ ├── merge2.vcf │ │ │ └── merge3.vcf │ │ │ ├── preprocessor │ │ │ ├── invalid-4.0.vcf │ │ │ └── valid-4.0.vcf │ │ │ ├── valid-4.0.vcf │ │ │ ├── valid-4.0.vcf.bz2 │ │ │ ├── valid-4.0.vcf.gz │ │ │ ├── valid-4.1-large.vcf │ │ │ ├── valid-4.1-large.vcf.gz │ │ │ ├── valid-4.2.vcf │ │ │ └── valid-4.2.vcf.gz │ ├── integration │ │ ├── __init__.py │ │ ├── bq_to_vcf_tests │ │ │ ├── README.md │ │ │ ├── no_options.json │ │ │ ├── option_allow_incompatible_schema.json │ │ │ ├── option_custom_sample_info_table.json │ │ │ ├── option_customized_export.json │ │ │ ├── option_number_of_bases_per_shard.json │ │ │ ├── option_preserve_sample_order.json │ │ │ ├── option_representative_header_file.json │ │ │ └── option_use_1_based_coordinate.json │ │ ├── preprocessor_tests │ │ │ ├── bgzf_preprocessor.json │ │ │ ├── header_conflicts_from_file.json │ │ │ ├── no_option_report_all_conflicts.json │ │ │ ├── non_splittable_bgzf_preprocessor.json │ │ │ ├── report_all_conflicts.json │ │ │ ├── report_inferred_headers.json │ │ │ └── report_malformed_records.json │ │ ├── run_bq_to_vcf_tests.py │ │ ├── run_preprocessor_tests.py │ │ ├── run_tests_common.py │ │ ├── run_vcf_to_bq_tests.py │ │ └── vcf_to_bq_tests │ │ │ ├── huge_tests │ │ │ └── test_1000_genomes.json │ │ │ └── presubmit_tests │ │ │ ├── large_tests │ │ │ └── test_non_splittable_gzip.temp_deleted_json │ │ │ ├── medium_tests │ │ │ ├── gnomad_genomes_GRCh37_chrX_head2500_run_vep.json │ │ │ ├── gnomad_genomes_GRCh38_chrX_head2500_run_vep_from_file.json │ │ │ ├── platinum_NA12877_hg38_10K_lines_run_vep.json │ │ │ ├── platinum_NA12877_hg38_10K_lines_run_vep_with_gc.json │ │ │ ├── platinum_no_merge.json │ │ │ ├── platinum_with_merge.json │ │ │ ├── test_1000_copies_of_valid_4_2_no_merge.json │ │ │ ├── test_1000_copies_of_valid_4_2_with_merge.json │ │ │ ├── test_annotation_pipeline_from_file_with_sharding.json │ │ │ ├── test_annotation_pipeline_from_file_with_sharding_1_based.json │ │ │ ├── test_annotation_pipeline_from_file_without_sharding.json │ │ │ └── test_splittable_gzip.temp_deleted_json │ │ │ └── small_tests │ │ │ ├── combine_from_multiple_inputs.json │ │ │ ├── incompatible_field_value.json │ │ │ ├── infer_header_fields.json │ │ │ ├── merge_option_1_based.json │ │ │ ├── merge_option_copy_filter_to_calls.json │ │ │ ├── merge_option_copy_quality_to_calls.json │ │ │ ├── merge_option_info_keys_to_move_to_calls_regex.json │ │ │ ├── merge_option_move_to_calls.json │ │ │ ├── merge_option_none.json │ │ │ ├── option_allow_malformed_records.json │ │ │ ├── option_allow_malformed_records_alternate_mismatch.json │ │ │ ├── option_append_to_table.json │ │ │ ├── option_append_to_table_sample_optimized.json │ │ │ ├── option_null_numeric_value_replacement.json │ │ │ ├── option_representative_header_file.json │ │ │ ├── option_split_alternate_allele_info_fields.json │ │ │ ├── option_update_schema_on_append.json │ │ │ ├── platinum_NA12877_hg38_10K_lines.json │ │ │ ├── platinum_partition_with_residual.json │ │ │ ├── platinum_partition_without_residual.json │ │ │ ├── valid_4_0_bz2.json │ │ │ ├── valid_4_0_gz.json │ │ │ ├── valid_4_0_gz_1_based.json │ │ │ ├── valid_4_1.json │ │ │ ├── valid_4_2.json │ │ │ ├── valid_4_2_VEP.json │ │ │ └── valid_4_2_gz.json │ ├── temp_dir.py │ ├── testdata_util.py │ └── vcf_header_util.py ├── transforms │ ├── __init__.py │ ├── annotate_files.py │ ├── bigquery_to_variant.py │ ├── bigquery_to_variant_test.py │ ├── combine_sample_ids.py │ ├── combine_sample_ids_test.py │ ├── densify_variants.py │ ├── densify_variants_test.py │ ├── extract_input_size.py │ ├── extract_input_size_test.py │ ├── filter_variants.py │ ├── filter_variants_test.py │ ├── fusion_break.py │ ├── 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