| Table | Field | Change notes |
|---|---|---|
| called_variants_nanopore | variant_types | added STR as enumerated value |
| called_variants_pac_bio | variant_types | added STR as enumerated value |
| genetic_findings | experiment_id | added 'see_notes' and 'see_MOD' as example values (this field will be required for validation) |
| genetic_findings | variant_type | added more specific enumerated values (possibly with delimiter) to match 'called_variants' tables |
| genetic_findings | pos | added note describing that this is .vcf-style coordinates |
| genetic_findings | pos | updated conditional requirement to align with variant_type change |
| genetic_findings | GREGoR_variant_classification | required if known disease gene |
| genetic_findings | gene_disease_validity_notes | required if known disease gene |
| genetic_findings | gene_disease_validity_notes | added; not required |
| genetic_findings | VRS_ID | added; not required |
| experiment_rna_short_read | depletion_targets | added; not required |
| called_variants_nanopore | chrom | added; not required |
| called_variants_pac_bio | chrom | added; not required |
| called_variants_optical_mapping | chrom | added; not required |
| aligned_nanopore | num_reads | changed data type to float for large number support |
| aligned_nanopore | num_bases | changed data type to float for large number support |
| aligned_nanopore | num_aligned_reads | changed data type to float for large number support |
| aligned_nanopore | num_aligned_bases | changed data type to float for large number support |
| aligned_nanopore | read_length_mean | changed data type to float |
| aligned_pac_bio | num_reads | changed data type to float for large number support |
| aligned_pac_bio | num_bases | changed data type to float for large number support |
| aligned_pac_bio | num_aligned_reads | changed data type to float for large number support |
| aligned_pac_bio | num_aligned_bases | changed data type to float for large number support |
| aligned_pac_bio | read_length_mean | changed data type to float |
| analyte | analyte_type | added PBMC as enumerated value |
| Table | Field | Change notes |
|---|---|---|
| called_variants_dna_short_read | chrom | added; not required |
| called_variants_nanopore | chrom | added; not required |
| called_variants_pac_bio | chrom | added; not required |
| called_variants_optical_mapping | chrom | added; not required |
| Table | Field | Change notes |
|---|---|---|
| experiment_optical_mapping | all | table added |
| molecule_file_optical_mapping | all | table added |
| aligned_molecules_optical_mapping | all | table added |
| aligned_assembly_optical_mapping | all | table added |
| optical_mapping_set | all | table added |
| called_variants_optical_mapping | all | table added |
| Table | Field | Change notes |
|---|---|---|
| genetic_findings | variant_type | added SV as allowable type |
| genetic_findings | sv_type | added; not required |
| genetic_findings | chrom | changed from required to conditional |
| genetic_findings | chrom_end | added; not required |
| genetic_findings | pos | changed from required to conditional |
| genetic_findings | pos_end | added; not required |
| genetic_findings | ref | changed from required to conditional |
| genetic_findings | alt | changed from required to conditional |
| genetic_findings | copy_number | added; not required |
| genetic_findings | gene_of_interest | renamed 'gene' field, made conditional, expanded notes |
| genetic_findings | hgvs | added; not required |
| genetic_findings | zygosity | added to list of allowable enumerations |
| genetic_findings | gene_disease_validity | added; not required |
| experiment_dna_short_read | sequencing_event_details | added; not required |
| Table | Field | Change notes |
|---|---|---|
| participant | gregor_center | add UCI to enumerated values |
| Table | Field | Change notes |
|---|---|---|
| participant | solve_status | change to enumerated values |
| Table | Field | Change notes |
|---|---|---|
| experiement_rna_short_read | total_reads | change data type to float to accommodate validation for numbers of reads >2^31 |
| genetic_findings | hgvsc | added; not required |
| genetic_findings | hgvsp | added; not required |
| genetic_findings | zygosity | added; not required |
| genetic_findings | known_condition_name | required if gene_known_for_phenotype = Known |
| genetic_findings | condition_id | required if gene_known_for_phenotype = Known |
| genetic_findings | condition_inheritance | required if gene_known_for_phenotype = Known |
| genetic_findings | partial_contribution_explained | required if phenotype_contribution = Partial |
| phenotype | syndromic | added; not required |
| aligned | aligned_file | will be populated by DCC in post-processing - no impact on data submitters. |
| aligned | aligned_file_index | will be populated by DCC in post-processing - no impact on data submitters. |
| experiment_dna_short_read | experiment_sample_id | field now required |
| experiment_dna_short_read | sequencing_event_details | added; not required |
| experiment_rna_short_read | total_reads | changed data type to float for large number support |
| experiment_nanopore | seq_library_prep_kit_method | added 'Unknown' ennumeration to allow for external data received where library prep kit is unknown |
| aligned_nanopore | quality_issues | added; not required |
| experiment_pac_bio | size_selection_method | added; not required |
| experiment_pac_bio | library_size | added; not required |
| experiment_pac_bio | smrt_cell_kit | added; not required |
| experiment_pac_bio | smrt_cell_id | added; not required |
| experiment_pac_bio | movie_name | added; not required |
| experiment_pac_bio | polymerase_kit | added; not required |
| experiment_pac_bio | sequencing_kit | added; not required |
| experiment_pac_bio | movie_length_hours | added; not required |
| experiment_pac_bio | includes_kinetics | added; not required |
| experiment_pac_bio | includes_CpG_methylation | added; not required |
| experiment_pac_bio | by_strand | added; not required |
| Table | Field | Change notes |
|---|---|---|
| genetic_findings | all | table added |
| experiment_pac_bio | all | table added |
| aligned_pac_bio | all | table added |
| aligned_pac_bio_set | all | table added |
| called_variants_pac_bio | all | table added |
| experiment_atac_short_read | all | table added |
| aligned_atac_short_read | all | table added |
| called_peaks_atac_short_read | all | table added |
| allele_specific_atac_short_read | all | table added |
| experiment | table_name | DCC added 'experiment_nanopore, experiment_pac_bio, and experiment_atac_short_read' as valid experiment types - no impact to data submitters. |
| aligned | all | table added - will be populated by DCC in post-processing - no impact on data submitters. |
| participant | solve_status | required field added |
| participant | missing_variant_case | required field added |
| participant | missing_variant_details | optional field added |
| Table | Field | Change notes |
|---|---|---|
| experiment_nanopore | all | table added |
| aligned_nanopore | all | table added |
| aligned_nanopore_set | all | table added |
| called_variants_nanopore | all | table added |
| aligned_dna_short_read | all | DCC added 'Is Unique' column to data model document to support validation - no impact to data submitters. |
| called_variants_dna_short_read | all | DCC added 'Is Unique' column to data model document to support validation - no impact to data submitters. |
| aligned_rna_short_read | all | DCC added 'Is Unique' column to data model document to support validation - no impact to data submitters. |
| aligned_nanopore | all | DCC added 'Is Unique' column to data model document to support validation - no impact to data submitters. |
| called_variants_nanopore | all | DCC added 'Is Unique' column to data model document to support validation - no impact to data submitters. |
| Table | Field | Change notes |
|---|---|---|
| analyte | analyte_processing_details | optional field added |
| analyte | primary_biosample | added allowable values to ennumeration |
| analyte | quality_flag | optional field added |
| experiment | all | table added |
| aligned_dna_short_read | mean_coverage | updated description |
| aligned_dna_short_read | any_qc_issues | optional field added |
| aligned_rna_short_read | all | table added |
| experiment_rna_short_read | all | table added |
| all | enumerated fields | required fields cannot have missing values; optional fields can have missing or blank values and do not have 'Unknown' as a separate option |
| participant | affected_status | made required |