IGV stalled when zooming in

[Chantal]

Hi,

When I start IGV it says “Warning: IGV is running with low available memory (226Mb)”. I can load my data file (.vcf.idx), but as soon as I try to zoom into a region (e.g. chromosome), it stalls forever.

I am using IGV_2.3.91 on Windows 7

Thank you

[James Robinson]

Hi,  

First you should not load the .vcf.idx file,   that is an index that will be loaded automatically.   Try loading the .vcf file alone.

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[Chantal]

Thanks Jim. I tried that too but the result is the same. Any other suggestions ?

On Wednesday, May 31, 2017 at 6:45:23 AM UTC+2, Jim Robinson wrote:

Hi,  

First you should not load the .vcf.idx file,   that is an index that will be loaded automatically.   Try loading the .vcf file alone.

On Tue, May 30, 2017 at 8:45 AM, Chantal <chantal...@erasme.ulb.ac.be> wrote:

Hi,

When I start IGV it says “Warning: IGV is running with low available memory (226Mb)”. I can load my data file (.vcf.idx), but as soon as I try to zoom into a region (e.g. chromosome), it stalls forever.

I am using IGV_2.3.91 on Windows 7

Thank you

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[James Robinson]

What method are you using to start IGV?  

[Chantal]

A shortcut on my desktop to IGV_2.3.91, which is in my program files

[James Robinson]

This doesn't really answer the question,  we don't distribute a shortcut.  We have the option to start from "Java Web Start" buttons on the website, or download a zipped binary package and run from a ".bat" file.    These are the only options that allocate a reasonable amount of memory,  running the "igv.jar" file directly, for example, will not.

So how was the program installed?  Are you using our ".bat" file?

Jim

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[Chantal]

I previously downloaded the program; the shortcut I installed indeed links to the .jar file. Can you say where amongst all the files in the download I can find the .bat file ?

I also tried the Launch with 1.2Gb button on the website now, but that still does not seem to solve the problem.
NB: my genome file is about 30Gb, could that be the problem ? If yes, is there a way to split it into separate smaller files ? The file contains WES data of over 100 patients. Can I for instance load the genome of an individual patient ? Thanks !

On Thursday, June 8, 2017 at 10:21:55 AM UTC+2, Jim Robinson wrote:

This doesn't really answer the question,  we don't distribute a shortcut.  We have the option to start from "Java Web Start" buttons on the website, or download a zipped binary package and run from a ".bat" file.    These are the only options that allocate a reasonable amount of memory,  running the "igv.jar" file directly, for example, will not.

So how was the program installed?  Are you using our ".bat" file?

Jim

On Thu, Jun 8, 2017 at 12:32 AM, Chantal <Chantal...@erasme.ulb.ac.be> wrote:

A shortcut on my desktop to IGV_2.3.91, which is in my program files

On Wednesday, June 7, 2017 at 2:08:55 AM UTC+2, Jim Robinson wrote:

What method are you using to start IGV?  

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[James Robinson]

The instructions for the download packages ("binary" and "windows") are on the web page.   Running igv.jar directly is not going to work,  and the 1.2 gb option probably will not as well for a file this size.   Follow the instructions posted and it should work.   I routinely load WGS VCFs with > 1,000 patients  (thousand genomes).

Secondly for VCF this large I would suggest indexing it with "tabix",  which comes with samtools.   The IGV index (.idx) file will work but is not as efficient.

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