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.
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.
>> 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,
>> 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.
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Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at: