Loading error: " Failed to create index from stream"....

[Stéphanie Thibault]

Hi,

I'm trying to use IGV for the first time. My vcf file is on my computer, but I get an error message when I load it:

Error loading C:\Users\...\H7JCD8PAU.mm2.sortdup.bqsr.hc.vcf: Failed to create index from stream., for input source: C:\Users\...\H7JCD8PAU.mm2.sortdup.bqsr.hc.vcf    

See the directory below. The last entry is a TBI file, so I wonder why the index cannot be created...

Thanks in advance for the help!

[igv-help]

The screenshot indicates the TBI index file is named differently from the other files. If you want to use the TBI index, load the vcf.gz file and make sure the TBI index file has the same name except for the .tbi part at the end. Remove the "TBI--" from the beginning of the index filename.

[Stéphanie Thibault]

I made sure the file name is the same except for the .tbi and tried loading again. I got this message:

An index file for [file name] could not be located. An index is recommended to view files of this size.   Click "Go" to create one now or "Cancel to proceed without an index.

And the error message showed up again. 

An IDX file was created, but I can't load the VCF.

I tried putting a shorter file names, with one ending in .vcf and one in .vcf.tbi: same thing happens. I tried deleting de IDX file, same error. I tried naming the files again to [filename].vcf and [filename].tbi (instead of .vcf.tbi), same thing...

I reloaded the file from the source, it didn't solve the problem.

[igv-help]

How did you create the tbi index in the first place? I saw a vcf.gz file in the screenshot.

So I assume you (or somebody else for you) bgzip'ed the original vcf file and then ran tabix on the .gz file to create the .tbi index.

The filename.vcf.gz file and the filename.vcf.gz.tbi file are a pair, and should have the same "filename". 

You should then load the vcf.gz file into IGV - not the original .vcf file.

[Stéphanie Thibault]

It finally worked... but not totaly. I can see the track name on the left, but no information seems to show. I checked for the reference genome: it's the right one. 

[igv-help]

As the message says, you have select a chromosome and zoom into a smaller region.  IGV can't load and display the whole file at once.