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CHANGELOG.md

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seqr Changes

dev

10/28/24

  • Update RNA Tissue Type choices (REQUIRES DB MIGRATION)

9/19/24

  • Update Biosample choices (REQUIRES DB MIGRATION)
  • Add support for Azure OAuth

8/14/24

  • Remove ONT support (REQUIRES DB MIGRATION)
  • Add "Validated Name" functional tag (REQUIRES DB MIGRATION)

8/9/24

  • Update directory structure for search backend

8/2/24

  • Adds index_file_path to IGV Sample model (REQUIRES DB MIGRATION)

7/24/24

  • Split RNA Sample models (REQUIRES DB MIGRATION)

7/8/24

  • Add VLM contact for Projects (REQUIRES DB MIGRATION)

6/11/24

  • Add "Partial Phenotype Contribution" functional tag (REQUIRES DB MIGRATION)

5/24/24

  • 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

5/8/24

  • Adds dynamic analysis groups (REQUIRES DB MIGRATION)

4/4/24

  • 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>
  • Support FRASER2 data (REQUIRES DB MIGRATION)
  • Add solve_status to Individual model (REQUIRES DB MIGRATION)
  • Update data deployment for hail backend to disk snapshots

3/13/24

  • Add "Probably Solved" analysis status (REQUIRES DB MIGRATION)

3/1/24

  • Add subscribable project notifications (REQUIRES DB MIGRATION)

1/8/24

  • Support OMIM entries with no associated gene and remove phenotypic_series_number (REQUIRES DB MIGRATION)

11/21/23

  • Support AIP upload
    • To add the required tag type, run ./manage.py loaddata new_variant_tag_types

11/13/23

  • Add Partial Solve analysis status in Family model (REQUIRES DB MIGRATION)

10/19/23

  • Migrate Family post_discovery_omim_number to integer array (REQUIRES DB MIGRATION)
  • Add GeneShet model to the reference DB (REQUIRES DB MIGRATION)

10/6/23

  • Require tissue_type in Sample model (REQUIRES DB MIGRATION)

9/22/23

  • Update VARIANTS dataset_type in Sample model (REQUIRES DB MIGRATION)

8/22/23

  • Add db indices to optimize RNA data queries (REQUIRES DB MIGRATION)

7/11/23

  • Add internal UI to trigger airflow data loading
  • Add RnaSeqSpliceOutlier display

6/23/23

  • Add a 'rank' field to the RnaSeqSpliceOutlier model (REQUIRES DB MIGRATION)
  • Remove hail python dependency

6/2/23

  • Update Clinvar filtering and display

  • Add support for Gencode v39

    • To add new data, run the update_gencode_latest

4/26/23

  • Add RnaSeqSpliceOutlier model (REQUIRES DB MIGRATION)
  • Add db index to improve Rna Sample Metadata performance (REQUIRES DB MIGRATION)

2/24/23

  • Updated Gregor sample manifest (REQUIRES DB MIGRATION)
  • Bumps python to 3.9

2/15/23

  • Support sharded VCFs in AnVIL loading

1/11/23

  • Require PHI disclaimer when uploading AnVIL pedigree

11/9/22

  • Add PhenotypePrioritization model (REQUIRES DB MIGRATION)

  • Add Refseq and MANE transcript info (REQUIRES DB MIGRATION)

    • To add new data, run the update_gencode_transcripts and update_refseq commands

10/13/22

  • Link MME submissions to saved variants (REQUIRES DB MIGRATION)

9/28/22

  • 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

9/6/22

  • Disable mixed authorization for local and AnVIL permissions (REQUIRES DB MIGRATION)

8/23/22

  • Add consent code for projects (REQUIRES DB MIGRATION)

7/19/22

  • Add "Incomplete Penetrance" functional tag type (REQUIRES DB MIGRATION)

7/12/22

  • Add MITO dataset type (REQUIRES DB MIGRATION)

6/23/22

  • Migrate RGP case note formatting (REQUIRES DB MIGRATION)

5/2/22

  • Add db indices for RNAseq outlier models (REQUIRES DB MIGRATION)

4/25/22

  • Trigger airflow DAG on AnVIL loading request

4/19/22

  • Add data type to family analysed by (REQUIRES DB MIGRATION)
  • Add ClinGen reference data (REQUIRES DB MIGRATION)

4/11/22

  • Remove pre-built static assets (REQUIRES IMAGE UPDATE)

3/25/22

  • Update display for translocations

3/18/22

  • Disallow deleting individuals in matchmaker (REQUIRES DB MIGRATION)
  • Add GenCC reference data (REQUIRES DB MIGRATION)
  • Update local pipeline to use latest clinvar

3/10/22

  • Return hom alt SNPs in trans with Deletions as compound hets
  • Disable variant download in demo projects (REQUIRES DB MIGRATION)

3/2/22

  • 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

2/4/22

  • Show RNA-seq expression data (REQUIRES DB MIGRATION)
  • Allow deletion of analysed families (REQUIRES DB MIGRATION)
  • Allow bulk updating assigned analysts

1/27/22

  • Separate structural annotation search for gCNV and genome SVs

1/26/22

  • Improved usage for docker-compose pipeline runner
  • Add support for serving the django media root out of a google cloud storage bucket

1/21/22

  • Support setting explicit order for saved search display (REQUIRES DB MIGRATION)

1/7/22

  • Update variant layout
  • Project page performance optimization

12/24/21

  • Show RNA-seq outlier data (REQUIRES DB MIGRATION)

12/07/21

  • Show delay warning on AnVIL loading requests

11/23/21

  • 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

11/17/21

  • Update pathogenicity search to override frequency filters
  • Add ACMG classifier to variants (REQUIRES DB MIGRATION)

11/10/21

  • Update in-silico score filtering behavior and add splice AI override

10/25/21

  • Add search filtering by in-silico score

10/21/21

  • Support updated WES SV loading pipeline format

9/30/21

  • 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)

9/17/21

  • Change family note fields into lists of notes (REQUIRES DB MIGRATION)
  • Add Panel App gene list integration (REQUIRES DB MIGRATION)

9/10/21

  • Use google storage API instead of gsutil for IGV

9/3/21

  • Add last updated information for family analysis_status (REQUIRES DB MIGRATION)

8/25/21

  • Better validation for MME match results
  • Send notification when adding dataset

8/20/21

  • Support loading/ searching data using ES aliases
  • Added changelog