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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


30th April 2019: Structural Variant Paths in the cancer_analysis table.

The paths to two structural variant VCFs from the cancer_analysis table are incorrectly given. Please use the file paths specified below:


Tumour sample plate-keyIncorrect path in LabKeyCorrect path to use
LP3000608-DNA_A01/genomes/by_date/2018-01-04/CX03028199/LP3000608-DNA_A01/Assembly/LP3000608-DNA_A01.bamSomaticVariations/000608-DNA_A01.ba_608-DNA_A01/Assem.somatic.SV.vcf.gz/genomes/by_date/2017-12-14/HX03028200/CancerLP3000608-DNA_A01_NormalLP3000607-DNA_A01/SomaticVariations/LP3000607-DNA_A01_LP3000608-DNA_A01.somatic.SV.vcf.gz
LP3000354-DNA_C01/genomes/by_date/2017-03-31/CF02206571/LP3000354-DNA_C01/Assembly/LP3000354-DNA_C01.bamSomaticVariations/000354-DNA_C01.ba_354-DNA_C01/Assem.somatic.SV.vcf.gz/genomes/by_date/2017-04-03/CF02206572/CancerLP3000354-DNA_C01_NormalLP3000334-DNA_C01/SomaticVariations/LP3000334-DNA_C01_LP3000354-DNA_C01.somatic.SV.vcf.gz









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