Integrative Genome Viewer (IGV)¶
The Integrative Genomics Viewer (IGV) is a high-performance, easy-to-use, interactive tool for the visual exploration of genomic data created by the Broad Institute. Due to its wide use in genomics, we have made verion 2.18.2 of this tool available within the Research Environment.
Reference genome files¶
Reference genomes and gene annotation for GRCh38/hg38 and GRCh37/hg19 have been recovered and made available to IGV from within the RE filesystem as the IGV site has not been whitelisted. On first launch the genomes will not be immediately visible and you will need to select them by following Genomes -> Load Genome from File ... -> public_data_resources -> IGV. Once the genomes have been loaded you can easily access these by selecting the assembly at the top left on subsequent launches of the IGV software.
The files are identical to those automatically recovered by IGV outside of the RE and can be used in the same way. However, this will result in an error message when you load IGV - you can just dismiss this.
Load your data¶
You can load genomic data from Genomics England to view in IGV. You can select File -> Load from file to click through to the file location. However, it is usually easier to select File -> Load from URL and paste in the file location, such as those you can find in the genome_file_paths_and_types table in LabKey.