I am unable to get VCF files to display in IGV in my local galaxy
installation. BAM files display fine, however, whenever I click on the
link to display a VCF file I get the following error message:
"You must import this dataset into your current history before you
can view it at the desired display application."
When I return to Galaxy, my history is indeed changed to a new empty
history.
I think this may have to do with the fact that I had to setup Apache to
allow unauthenticated access to the bam/vcf files (see my notes on how I
did this at
https://sites.google.com/site/princetonhtseq/tutorials/visualization-with-galaxy-and-igv/igv-as-a-display-application-in-galaxy).
However, I can't figure out why BAM files work and VCF files don't. Any
advice or insight would be appreciated.
--
Lance Parsons - Scientific Programmer
134 Carl C. Icahn Laboratory
Lewis-Sigler Institute for Integrative Genomics
Princeton University
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