Question: Loading VCF into a local IGV fails with metadata error during data prep step
1
gravatar for kry_8
6 months ago by
kry_810
kry_810 wrote:

Although my genome sequence is part of the list of options thanks to custom build, the link to display the results is not being updated. I was wondering if this is because I am not limiting the search to a specific part of the genome and instead I am trying to see all the variants in IGV. In the past, I have done only with the BWA-MEM file and then looking at it in IGV and look for the variants manually. I thought with FreeBayes and Variant Filter I would be able to see the variants only. Is it possible or is it only possible for a selected region of the genome? Thanks!

loading igv vcf local custom • 208 views
ADD COMMENTlink modified 6 months ago by Jennifer Hillman Jackson25k • written 6 months ago by kry_810

Yes, all of this should be possible (full genome loaded into IGV, VCF display [including filtered], Custom genome/build, etc).

There were some server issues over the weekend in the process of being corrected. These might be impacting the IGV local display function. Once done, I'll see if I can reproduce the issue. More feedback soon.

ADD REPLYlink modified 6 months ago • written 6 months ago by Jennifer Hillman Jackson25k
0
gravatar for Jennifer Hillman Jackson
6 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

Launching IGV is successful again now for most datatypes. I found one new problem with VCF dataset loading and am testing a few more use-case.

You could try again now as well. Should that fail, then we will need to fix the loading issues on our side before you can visualize in IGV.

Progress on the tests/corrections will post back to the tracking ticket: https://github.com/galaxyproject/usegalaxy-playbook/issues/89

Thanks for reporting the problem!

Jen, Galaxy team

ADD COMMENTlink modified 6 months ago • written 6 months ago by Jennifer Hillman Jackson25k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 145 users visited in the last hour