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Merge pull request #30 from UW-GAC/v1.5
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version 1.5
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@smgogarten
smgogarten authored May 9, 2024
2 parents bd9ab7d + 9cd9f8d commit 8deda54
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126 changes: 79 additions & 47 deletions CHANGELOG.md
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# Change log

## 1.5

|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 |


## 1.4.2

|Table |Field |Change notes |
|:-----------|:-------------|:----------------------------|
|participant |gregor_center |add UCI to enumerated values |


## 1.4.1

|Table |Field |Change notes |
|:-----------|:------------|:---------------------------|
|participant |solve_status |change to enumerated values |


## 1.4

|Table |Field |Change notes |
|:--------------------------|:---------------------------|:--------------------------------------------------------------------------------------------------|
|experiement_rna_short_read |total_reads |change data type to float to accommodate validation for numbers of reads >2^31 |
|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 |
|participant |solve_status |change to enumerated values |
|participant |gregor_center |add UCI 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 |


## 1.3

|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 |
|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 |
|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 |


## 1.2
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