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Question: UCSC Genome Browser not loading VCF files
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gravatar for ajimenez
9 months ago by
ajimenez • 0
ajimenez • 0 wrote:

Since 23 Feb I cannot view my VCF files on the UCSC Genome Browser. When I click on the Main link the browser opens, but the user track just shows the address of the link (http...) and not the variants. This problem only happens when I try to load my previous VCF files (1-3 weeks old). The files themselves are fine, since they can be displayed properly when I use them out of Galaxy.

get-data ucsc vcf table-browser browser • 355 views
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modified 6 months ago by Jennifer Hillman Jackson ♦ 25k • written 9 months ago by ajimenez • 0

Hi - I am doing some testing. More feedback soon and thanks for reporting the problem. Jen, Galaxy team

ADD REPLY • link written 9 months ago by Jennifer Hillman Jackson ♦ 25k

Today I have checked the VCF files again and one of them (produced with snpEff) has worked fine after been reloaded by the browser. The other two VCF files (produced with Varscan and Freebayes) still do not work and just show the link (http...).

ADD REPLY • link written 9 months ago by ajimenez • 0
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gravatar for Jennifer Hillman Jackson
6 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

The issues with VCF display in a couple of external applications have been ticketed as problems. These include UCSC, IOBIO, and a local IGV. The workaround, for now, is to download the VCF data with display problems and load them directly into the external applications.

Thanks for reporting the problem! Jen, Galaxy team
ADD COMMENT • link written 6 months ago by Jennifer Hillman Jackson ♦ 25k
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