Problem in uploading hg37/hg19

[sania Rauf]

Dear Team

I tried to upload Hg37 but its keep saying " The genome 'Human (GRCh37/hg19)' could not be read. "is there any problem in server? because even i cannot upload my bam files to read on IGV

Kind regards

Sania

[igv-help]

Are you still having this problem? Everything seems to be ok on our end.

Helga

[Paul Avalos]

Hello, I am not the original poster but we are having a similar/same issue

We are currently using IGV 2.12.3. When opening the Desktop app, we receive "Error loading genome: hg19". Pressing OK gives us " Unexpected error:null. See igv.log for more details". I do not know where to find igv.log

Clicking on Hg19 from the top left gives "The genome [Hg19] could not be read. Would you like to remove the selected entry?".

I have also tried Going to Genomes>Select Hosted Genomes and receive the error " Warning: could not connect to the genome server (https:\\s3.amazonaws.com/igv.org.genomes/genomes.tsv) Or locally defined genomes will be available." This opens to a "Hosted Genomes" window that is blank with nothing to select. I'm not sure if this is related.

Thank you,

Paul

[igv-help]

Hi Paul,

The Amazon host that supported older versions of IGV (> 5 years old) is being decommissioned.   To fix this problem you need to edit your preferences.   Specifically select "View > Preferences > Advanced tab".   There is a field on this tab for the "Genome Server URL".   Replace the entry there with the following

https://igv.org/genomes/genomes.tsv

You might run into other issues,  I will help you work around them, but this is the first step.

-- Jim