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Merge pull request #32 from UW-GAC/v1.6.1
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redo v1.6: reinstate SNV/INDEL as allowed value for genetic findings
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@smgogarten
smgogarten authored Sep 10, 2024
2 parents 06f253a + 75fbc58 commit d5f51e4
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53 changes: 27 additions & 26 deletions CHANGELOG.md
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## 1.6

|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 |changed allowable values to match other 'called_variants' tables (SNV, INDEL as separate values posssibly with delimiter instead of SNV/INDEL |
|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 |
|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 |


## 1.5.2
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6 changes: 3 additions & 3 deletions GREGoR_data_model.json
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"column": "variant_type",
"required": true,
"data_type": "enumeration",
"enumerations": ["SNV", "INDEL", "SV", "CNV", "RE", "MEI", "STR"],
"enumerations": ["SNV/INDEL", "SV", "RE", "SNV", "INDEL", "CNV", "MEI", "STR"],
"multi_value_delimiter": "|",
"examples": "SNV|CNV",
"notes": "SNV: single nucelotide variants\nINDEL: short insertion/deletions (<50bp)\nRE: repeat elements\nSV: structural variants, including copy number variants and mobile element insertions"
"notes": "SNV/INDEL: single nucelotide variants or short insertion/deletions (<50bp)\nRE: repeat elements\nSV: structural variants, including copy number variants and mobile element insertions"
},
{
"column": "sv_type",
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"required": true,
"description": "analyte derived from the primary_biosample. The actual thing you're sticking into a machine to analyze/sequence",
"data_type": "enumeration",
"enumerations": ["DNA", "RNA", "cDNA", "blood plasma", "frozen whole blood", "high molecular weight DNA", "urine"],
"enumerations": ["DNA", "RNA", "cDNA", "blood plasma", "frozen whole blood", "high molecular weight DNA", "urine", "PBMC"],
"examples": "DNA"
},
{
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