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 2.19.7 of this tool available within the Research Environment.
Reference genomes¶
The first time IGV starts it will load the remote "Human (GRCh38/hg38)" reference genome. To load another reference genome, and/or download a local copy to speed up loading next time, choose Genomes → Download Hosted Genome... and check the Download sequence and Download annotations options.
If you encounter any issues with downloading or using a remote reference genome, you can also load a reference genome provided in public_data_resources, via Genomes → Load from File... and choose /public_data_resources/IGV/hg38/hg38_local.json or /public_data_resources/IGV/hg19/hg19_local.genome. Note that annotations included with these are less recent than the remotely available reference genomes.
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.
Known Issues¶
IGV hangs or displays an error when trying to load a somatic structural variant (SV) VCF
When I try to load a somatic SV VCF file from the Dragen 3.2.22 pipeline (referenced by the cancer_100k_genomes_realigned_on_pipeline_2 table in Labkey), IGV hangs or displays an "Unexpected error: Java heap space" error. Older somatic SV VCFs from the NSv4 pipeline are loading fine.
the index file (.tbi) that accompanies somatic SV VCF files from the Dragen 3.2.22 pipeline are not compatible with IGV. The same index files appear to work fine with other tools, but appear to cause an infinite loop in IGV. The work-around is to create a symlink to the VCF file in your home directory and (optionally) re-index the VCF. Example:
ln -sf /genomes/by_date/<date>/<delivery id>/<directory>/<filename>.somatic.SV.vcf.gz <filename>.somatic.SV.vcf.gz
bcftools index -t <filename>.somatic.SV.vcf.gz
File → Load from File... and navigating to your home directory.