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4th April 2019: IGV Genome Browser

The Broad Institute have changed where they host the genome files for IGV (from igvdata.broadinstitute.org/* to https://s3.amazonaws.com/igvdata.broadinstitute.org/*). As the latter is not yet 'white-listed' within the Research Environment, the genome files will not be accessible causing an error to occur when attempting to load them within IGV. 

We have manually downloaded the FASTA, RefSeq annotation, chromosome cytoband, and chromosome aliases from the Broad for hg19/GRCh37 and hg38/GRCh38 reference assemblies and have created .genome files from them. These are identical to the default ones present in IGV and can be loaded into IGV using the instructions below.

Step #InstructionScreenshot
1Open the IGV application from the desktop-
2Click 'Cancel' on the subsequent pop-up box

3On the IGV toolbar, navigate to 'Genomes' > 'Load Genome from File...'

4In the file browser, navigate to 'Home' > 'public_data_resources'

5Navigate to 'IGV'

6Select the reference assembly of choice (hg19/GRCh37 or hg38/GRCh38).

7Click on the corresponding '.genome' file.

8This will load the genome file selected as a local version



5th March 2019: 

An issue was identified in the main-programme_v6_2019-02-28 data release regarding incorrect file paths to 2,204 genomes. This issue caused the time-stamp of the genome delivery date to be incorrect by 24hours; which in turn resulted in incorrect file paths for these genomes. The impact of this issue is that users are unable to access these genomes.  The tables affected in the v6 data release are sequencing_report, genome_file_paths_and_types and rare_disease_analysis. The incorrect paths have been identified and are available within the Research Environment on the Live Issues tab of the Research Environment Documentation. The Research Environment Documentation can be accessed from within the Research Environment via the desktop link. We will be applying a permeant fix to the issue which will result in these three tables within LabKey being unavailable for a short period of time.  We will provide advance notice of when the fix will be applied. Apologies for any inconvenience caused.

7th March 2019: 

New /gel_data_resources/ data for main-programme_v6_2019-02-28 data release for the cancer_analysis table have not yet been imported into the final location, e.g.: /gel_data_resources/main_programme/normalised_vcf_cancer/GRCh38. These will be made available within the next week. Apologies for any inconvenience caused.

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