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5th August 2019: Duplicate rows in the cancer_analysis table

There are seven completely duplicated rows in the cancer_analysis table. The interpretation request IDs for these duplicated rows are: 15807-1, 21450-1, 22977-1, 14581-2, 30736-1, 31083-1, 42295-1. Please ensure these are considered in any analysis. 

5th August 2019: Participant with incorrect gender in the cancer_analysis table

A participant has been identified with incorrect gender assignment in the cancer_analysis table. The participant has two interpretation request IDs for two different tumour-normal pairings. The IDs are: 14497-1 and 48870-1. As a rule of thumb, please use the latest interpretation request ID (48870-1) in all cases for the correct gender assignment. 

31st July 2019: LabKey API

The Rlabkey R package for querying LabKey contains a bug whereby only the first 100,000 rows of a table are imported when using the labkey.selectRows() function (even when the maxRows argument is set to > 100,000). 

To work around this issue, please use the labkey.executeSql() function instead. For example, to select the entire sequencing_report table for the Main Programme V7 release, use the following code:

labkey.setDefaults(baseUrl = "")

sequencing_report <- labkey.executeSql(
    folderPath = "/main-programme/main-programme_v7_2019-07-25",
    schemaName = "lists",
    colNameOpt = "rname", 
    maxRows = 10000000,
    sql = "SELECT * FROM sequencing_report")

Please see: Using the LabKey API for more SQL examples. 

4th April 2019: IGV Genome Browser

The Broad Institute have changed where they host the genome files for IGV (from* to*). 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

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