Latest TRE data updates and changes¶

(newest shown first)

2025-OCT-23 by MA¶

Volume mounts that show up on desktop while using modules are now hidden.

2025-OCT-22 by MA¶

Removed unused .html files from desktop.

2025-OCT-08 by MA¶

Added a new module named tre-python3.13 that contains python3.13, updated polars version to 1.33 and latest versions of previous python packages in TRE.

2025-SEP-23 by MA¶

Upgraded the VM base OS from debian 11 to debian 12.

Introduced the new modular software management tool called 'Module Manager': https://genes-and-health.github.io/TRE-docs/using-the-tre/module-manager-guide/

2025-SEP-18 by SR¶

Release of the new G&H TRE documenation website: https://genes-and-health.github.io/TRE-docs/

2025-MAY-20 by DVH¶

Begun release of 55k exome ExWAS to Consortium1 partners. Quant traits initially, to be followed by binary traits.
gs://qmul-production-library-consortiumpriorityperiod-red
└── Callsets
    └── 2024_05_55kCallset
        └── release_2025-JUN-16_ExWAS/

2025-MAY-05 by DVH¶

Released 51k GSA-TOPMEDr3 GWAS results for v010 quant traits

gs://qmul-production-library-red
└── genesandhealth
    └── GSAv3EAMD
        └── Jan2024_51k_TOPMED-r3_Imputation_b38
            └── 2025_05_v010_quantpy_GSATOPMEDr3_GWAS/

2025-APR-28 by RK¶

Improved the file dialog that allows users to upload files to the red bucket. Users can now upload files to the red bucket in the directory of their choice and create a new directory in the red bucket if they wish.

2025-APR-24 by DVH¶

More Barts Health datafiles from 2024_09 release redaacted and put in the TRE

gs://qmul-production-library-red
└── genesandhealth
    └── phenotypes_rawdata
        └── DSA__BartsHealth_NHS_Trust
            └── 2024_09_ResearchDataset/

2025-APR-24 by DVH¶

New quant traits v010 uploaded:

gs://qmul-production-library-red
└── genesandhealth
    └── phenotypes_curated
        └── version010_2025_04/

2025-MAR-26 by DVH¶

Uploaded new NHS England (ex Digital) HES data. More datasets still to come.
gs://qmul-production-library-nhsdigital-sublicence-red
└── DSA__NHSDigitalNHSEngland
    └── 2025_03/

2025-MAR-26 by DVH¶

Uploaded new folder of gvcf files from exome sequencing. These are the input to variant joint calling. They are unfiltered samples and genotypes, do not use for genetic association studies!
gs://qmul-production-library-consortiumpriorityperiod-red
└── gvcfs/

2025-MAR-25 by DVH¶

Removal of some files in previous Barts Health phenotypes_raw datasets, and replacement with more highly redacted versions:

Deleted:

gs://qmul-production-library-red
└── genesandhealth
    └── phenotypes_rawdata
       └── DSA__BartsHealth_NHS_Trust
           └── 2024_09_ResearchDataset
               └── RDE_Measurements.ascii.redacted.tab

Replaced with:

 gs://qmul-production-library-red
 └── genesandhealth
     └── phenotypes_rawdata
         └── DSA__BartsHealth_NHS_Trust
             └── 2024_09_ResearchDataset
                 └── RDE_Measurements.ascii.redacted2.tab

Deleted:

gs://qmul-production-library-red
└── genesandhealth
    └── phenotypes_rawdata
       └── DSA__BartsHealth_NHS_Trust
           └── 2023_12_ResearchDatasetv1.6
               └── GandH_Measurements__20240423.ascii.redacted.tab

Replaced with:

gs://qmul-production-library-red
└── genesandhealth
    └── phenotypes_rawdata
       └── DSA__BartsHealth_NHS_Trust
           └── 2023_12_ResearchDatasetv1.6
               └── GandH_Measurements__20240423.ascii.redacted2.tab

Deleted: - we do not think this file is used at all, so have not replaced.

gs://qmul-production-library-red
└── genesandhealth
    └── phenotypes_rawdata
       └── DSA__BartsHealth_NHS_Trust
           └── 2023_12_ResearchDatasetv1.6
               └── in-beta-testing
                   └── GH_RAW_Pathology__20231211.ascii.redacted.tab

Deleted:

gs://qmul-production-library-red
└── genesandhealth
    └── phenotypes_rawdata
       └── DSA__BartsHealth_NHS_Trust
           └── 2024_09_ResearchDataset
               └── RDE_Pathology.ascii.nohisto.redacted.csv

Replaced with:

gs://qmul-production-library-red
└── genesandhealth
    └── phenotypes_rawdata
       └── DSA__BartsHealth_NHS_Trust
           └── 2024_09_ResearchDataset
               └── RDE_Pathology.ascii.nohisto.redacted2.csv

Deleted:

gs://qmul-production-library-red
└── genesandhealth
    └── phenotypes_rawdata
       └── DSA__BartsHealth_NHS_Trust
           └── 2023_12_ResearchDatasetv1.6
               └── GH_Pathology__20231218.ascii.nohisto.redacted.tab

Replaced with:

gs://qmul-production-library-red
└── genesandhealth
    └── phenotypes_rawdata
        └── DSA__BartsHealth_NHS_Trust
            └── 2023_12_ResearchDatasetv1.6
                └── GH_Pathology__20231218.ascii.nohisto.redacted2.tab