Problem loading IGV in the Research Environment

Question

I have problems accessing IGV in the Research Environment. I get the message that the genome file cannot be read/loaded. How can the access be restored?

Answer

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 '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 manually. For a step-by-step guide on how to load these please follow the instructions here: Live Service Issues

Last updated

This page was last updated on the 20 Jan 2020.