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
Onderwerp: Re: [galaxy-dev] Share some code (xml) to wrap IGV itself as a
Galaxy visualizer
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
; jrobi...@broadinstitute.org
Onderwerp: Re: [galaxy-dev] Share some code (xml) to wrap IGV itself as a
Galaxy visualizer
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
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,
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,
