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seqr Changes

dev

3/1/26

  • Deprecate Elasticsearch support

2/25/26

  • Switches clickhouse to use new variant tables and deprecate old annotations tables (REQUIRES DB MIGRATION)
    • Note that for users with Clickhouse already enabled, this requires a manual intervention. See the seqr-helm documentation for more details.

2/11/26

  • Adds eigen reference data to clickhouse (REQUIRES DB MIGRATION)
    • Note that for users with Clickhouse already enabled, this migration will enqueue tasks in the loading pipeline. You may want to monitor the pipeline for any failures and re-trigger them in the event of any failures.
  • Updates VLM to the finalized v1 schema

1/8/26

  • Moves PanelApp updates from their own manage command into the main update_all_reference_data command. May require changes to custom cron jobs (REQUIRES DB MIGRATION)
  • Adds variant-level reference data to clickhouse (REQUIRES DB MIGRATION)
    • Note that for users with Clickhouse already enabled, this migration will enqueue tasks in the loading pipeline. You may want to monitor the pipeline for any failures and re-trigger them in the event of any failures.
  • Deprecates the "Gene Variant Lookup" page in favor of an "Include External Projects" option on the main search page

11/12/25

  • Changes support for RNA loading to accept unprocessed output from RNA callers, and moves loading to the project page. See documentation for more details.

10/27/25

  • Adds affected status to the gt stats views/dicts in Clickhouse (REQUIRES DB MIGRATION)
    • Note that for users with Clickhouse already enabled, this migration will enqueue tasks in the loading pipeline to refresh existing data. You may want to monitor the pipeline for any failures and re-trigger them in the event of any failures. seqr will contiunue to function normally if these steps are skipped, but in the long run this may result in inaccurate search results

9/18/25

  • Store gene ids on SavedVariant model (REQUIRES DB MIGRATION)

9/29/25

  • Deprecate hail backend support

8/7/25

  • Deprecate support for lifting existing projects from GRCH37 to GRCh38

4/4/25

  • Refactor manage commands to update reference data. May require changes to custom cron jobs. (REQUIRES DB MIGRATION)

11/21/24

  • Migrate "Submit to Clinvar" to generic report flag for Variant Notes (REQUIRES DB MIGRATION)

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
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