Uploading *.vcf data into IGV for the first time

[Lili Peng]

Hi,

I am trying to load the data into the 64-bit Java version of IGV but get the following message:

"An index file for ~\ExAC.r0.3.1.sites.vep.vcf could not be located. An index is required to view files of this size.   Click "Go" to create one now."

The *.vcf file is ~33GB, by the way.

So, I click 'Go' but IGV has been churning away at it for the past 7 min.

Any advice for a newbie would be greatly appreciated,
lili

[James Robinson]

It might take a few hours to index a 33GB file.  I highly recommend you use tabix to do the indexing rather than IGV,  it will also compress it.  No guarantees you’ll be able to load a VCF that size even after indexing.

Jim

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[Lili Peng]

Thanks for the advice on using tabix, as I've already downloaded the program onto my UNIX environment.

Would you know if there are any examples of indexing *.vcf genomics data using tabix?  The manual (http://www.htslib.org/doc/tabix.html) provides only a few examples.  It would be really helpful if I were to see more examples, especially complex and descriptive ones.

Thanks again,
Lili

[Jim Robinson]

I don't have anything to add beyond what's in the manual, which you've already found.   There's nothing really complex about it.  The VCF should be sorted by start position,  then bgzip it and run tabix on the bgzipped file.

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[Lili Peng]

I'd used tabix to generate a *.tbi file, but it's still unclear to me how to index the *.gz file using the *.tbi file with tabix.  Which is why I'd asked if there are more detailed examples.  I've been searching UCSC and other websites for specific steps, but each is all written involving a tool/web app specific to that website.

[Jim Robinson]

Hi,  I don't understand your question,  the .tbi file is the index.  If you have it just load the vcf.gz file into IGV or any other program that supports tabix indexes.   Keep the vcf.gz and vcf.gz.tbi files together in the same directory.

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