Hi Jim,

Yes, Galaxy ships the vcf files bgzip compressed (filename.vcf.gz) and makes a 
tabix index available along side (filename.vcf.gz.tbi). In the case of Galaxy, 
the pysam package is used to create the tabix index. 


Thanks,

Dan


On Jan 17, 2012, at 9:44 AM, Jim Robinson wrote:

> Hi Dan, thanks for the response.   Does Galaxy index VCF files, for example 
> with tabix of the "tribble" library?  IGV currently requires indexes for VCF 
> files, mainly because the ones we generate here are huge.   This could be 
> relaxed for smaller VCF files, and I have that on my list.
> 
> best,
> 
> Jim
> 
>> Hi Ming,
>> 
>> From Galaxy, you can currently view BAM and VCF (VCF is available in 
>> -central, but will be in the next -dist release) files within IGV.  To do 
>> this on a local set up, you will need to have your Galaxy instance behind a 
>> proxy (e.g. nginx or apache); this enables byte-range requests. In the 
>> datatypes_conf.xml file, make sure that '<display file="igv/bam.xml" />' and 
>> '<display file="igv/vcf.xml" />' are not commented out. Within Galaxy, your 
>> BAM or VCF file should have the dbkey set to a build that is configured to 
>> be viewable at IGV (see tool-data/shared/igv/igv_build_sites.txt).
>> 
>> Please let us know if we can provide additional assistance.
>> 
>> 
>> Thanks for using Galaxy,
>> 
>> Dan
>> 
>> 
>> On Jan 14, 2012, at 10:09 PM, bt.microzh...@gmail.com wrote:
>> 
>>> Hi Guys,
>>>     I am glad to hear form Jim Robinson that  exists some code could wrap 
>>> IGV as a Galaxy visualizer. Recently, i implemented local Galaxy instant 
>>> and wanted to integrate
>>> IGV as a visualizer. I'm looking forward your reply.
>>> 
>>> Regards,
>>> 
>>> Ming 
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> 

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