- Update RNA Tissue Type choices (REQUIRES DB MIGRATION)
- Update Biosample choices (REQUIRES DB MIGRATION)
- Add support for Azure OAuth
- Remove ONT support (REQUIRES DB MIGRATION)
- Add "Validated Name" functional tag (REQUIRES DB MIGRATION)
- Update directory structure for search backend
- Adds index_file_path to IGV Sample model (REQUIRES DB MIGRATION)
- Split RNA Sample models (REQUIRES DB MIGRATION)
- Add VLM contact for Projects (REQUIRES DB MIGRATION)
- Add "Partial Phenotype Contribution" functional tag (REQUIRES DB MIGRATION)
- Adds external_data to Family model (REQUIRES DB MIGRATION)
- Adds post_discovery_mondo_id to Family model (REQUIRES DB MIGRATION)
- Adds guid and created fields to PhenotypePrioritization model (REQUIRES DB MIGRATION)
- Enable "Reports" tab by default for local installations
- Adds dynamic analysis groups (REQUIRES DB MIGRATION)
- Add ability to import project metadata from gregor metadata
- Only enabled for a project if tag is first created via
./manage.py add_project_tag --name="GREGoR Finding" --order=0.5 --color=#c25fc4 --project=<project>
- Only enabled for a project if tag is first created via
- Support FRASER2 data (REQUIRES DB MIGRATION)
- Add solve_status to Individual model (REQUIRES DB MIGRATION)
- Update data deployment for hail backend to disk snapshots
- Add "Probably Solved" analysis status (REQUIRES DB MIGRATION)
- Add subscribable project notifications (REQUIRES DB MIGRATION)
- Support OMIM entries with no associated gene and remove phenotypic_series_number (REQUIRES DB MIGRATION)
- Support AIP upload
- To add the required tag type, run
./manage.py loaddata new_variant_tag_types
- To add the required tag type, run
- Add Partial Solve analysis status in Family model (REQUIRES DB MIGRATION)
- Migrate Family post_discovery_omim_number to integer array (REQUIRES DB MIGRATION)
- Add GeneShet model to the reference DB (REQUIRES DB MIGRATION)
- Require tissue_type in Sample model (REQUIRES DB MIGRATION)
- Update VARIANTS dataset_type in Sample model (REQUIRES DB MIGRATION)
- Add db indices to optimize RNA data queries (REQUIRES DB MIGRATION)
- Add internal UI to trigger airflow data loading
- Add RnaSeqSpliceOutlier display
- Add a 'rank' field to the RnaSeqSpliceOutlier model (REQUIRES DB MIGRATION)
- Remove hail python dependency
-
Update Clinvar filtering and display
-
Add support for Gencode v39
- To add new data, run the
update_gencode_latest
- To add new data, run the
- Add RnaSeqSpliceOutlier model (REQUIRES DB MIGRATION)
- Add db index to improve Rna Sample Metadata performance (REQUIRES DB MIGRATION)
- Updated Gregor sample manifest (REQUIRES DB MIGRATION)
- Bumps python to 3.9
- Support sharded VCFs in AnVIL loading
- Require PHI disclaimer when uploading AnVIL pedigree
-
Add PhenotypePrioritization model (REQUIRES DB MIGRATION)
-
Add Refseq and MANE transcript info (REQUIRES DB MIGRATION)
- To add new data, run the
update_gencode_transcripts
andupdate_refseq
commands
- To add new data, run the
- Link MME submissions to saved variants (REQUIRES DB MIGRATION)
- Add Gregor fields to sample manifest (REQUIRES DB MIGRATION)
- Deprecate auto-granting project access for analysts (removes ANALYST_PROJECT_CATEGORY env variable)
- Add support for adding user groups for project access
- Disable mixed authorization for local and AnVIL permissions (REQUIRES DB MIGRATION)
- Add consent code for projects (REQUIRES DB MIGRATION)
- Add "Incomplete Penetrance" functional tag type (REQUIRES DB MIGRATION)
- Add MITO dataset type (REQUIRES DB MIGRATION)
- Migrate RGP case note formatting (REQUIRES DB MIGRATION)
- Add db indices for RNAseq outlier models (REQUIRES DB MIGRATION)
- Trigger airflow DAG on AnVIL loading request
- Add data type to family analysed by (REQUIRES DB MIGRATION)
- Add ClinGen reference data (REQUIRES DB MIGRATION)
- Remove pre-built static assets (REQUIRES IMAGE UPDATE)
- Update display for translocations
- Disallow deleting individuals in matchmaker (REQUIRES DB MIGRATION)
- Add GenCC reference data (REQUIRES DB MIGRATION)
- Update local pipeline to use latest clinvar
- Return hom alt SNPs in trans with Deletions as compound hets
- Disable variant download in demo projects (REQUIRES DB MIGRATION)
- Update seqr dockerfile to improve immutability and build automation (REQUIRES IMAGE UPDATE)
- Adds NPM asset build to the seqr dockerfile
- Bumps major version of react/ redux
- Show RNA-seq expression data (REQUIRES DB MIGRATION)
- Allow deletion of analysed families (REQUIRES DB MIGRATION)
- Allow bulk updating assigned analysts
- Separate structural annotation search for gCNV and genome SVs
- Improved usage for docker-compose pipeline runner
- Add support for serving the django media root out of a google cloud storage bucket
- Support setting explicit order for saved search display (REQUIRES DB MIGRATION)
- Update variant layout
- Project page performance optimization
- Show RNA-seq outlier data (REQUIRES DB MIGRATION)
- Show delay warning on AnVIL loading requests
- Update the seqr Dockerfile base image from debian:stretch to python:3.7-slim-bullseye
- Consolidation and cleanup of various RUN tasks in the seqr Dockerfile
- Update pathogenicity search to override frequency filters
- Add ACMG classifier to variants (REQUIRES DB MIGRATION)
- Update in-silico score filtering behavior and add splice AI override
- Add search filtering by in-silico score
- Support updated WES SV loading pipeline format
- Allow project-specific HGMD access (REQUIRES DB MIGRATION)
- Demo project available to all users (REQUIRES DB MIGRATION)
- Update pedigree label display (requires manual cleanup for saved pedigree datasets)
- Support application downtime/ warning messages (REQUIRES DB MIGRATION)
- Change family note fields into lists of notes (REQUIRES DB MIGRATION)
- Add Panel App gene list integration (REQUIRES DB MIGRATION)
- Use google storage API instead of gsutil for IGV
- Add last updated information for family analysis_status (REQUIRES DB MIGRATION)
- Better validation for MME match results
- Send notification when adding dataset
- Support loading/ searching data using ES aliases
- Added changelog