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VCF file support

asked 2012-12-04 12:21:43 -0600

Chelsea Tolentino gravatar image

Do users have the ability to upload VCF files now? I read it should have been ready in November 2012.

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answered 2013-03-27 13:36:08 -0600

Support for VCF files was added with version 1.1.0 of GenomeBrowse. Single sample VCFs, multi-sample VCFs and even "site"-based VCFs with no sample data are now supported. SNVs and InDels are supported and we will do our best to draw Structural Variants, but their representation in VCF format is less standardized.

We incorporated a new rendering mode for multi-sample "Variant Maps", as well as auto-compression/indexing of VCF to Bgzip/Tabix format required to read files directly for rendering.

Currently any VCF file loaded into GenomeBrowse must be sorted.

Please update to the most recent version of GenomeBrowse to access all available features. To update GenomeBrowse please download the installer from our website.

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answered 2014-06-10 14:28:23 -0600

Hello Jami,

I am having trouble loading VCF and BAM files we have in the lab that have been analyzed in the past. When I try to drag and drop them into the viewer, I get a stop sign.

Is there any annotation inside the file I need to check?

Thanks

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answered 2014-06-09 11:42:16 -0600

Hi Tamar,

I am sorry you are having issues loading your BAM and VCF files into GenomeBrowse.

Have you tried loading them through the Add dialog by navigating to their saved location? Our records indicate that you are using the Win64 version, if that is correct there is a know bug in that version for visualizing BAM files which may be causing the issue.

Can you try updating to GenomeBrowse 2.0.2 to see if that resolves the issue. You can download the installer from our website at the following link. http://www.goldenhelix.com/GenomeBrowse/index.html

If you are still seeing the same issues after updating could provide some screenshots of the error message, or even provide a sample of the data so we can try and reproduce the issue.

You can email me directly at genomebrowse@goldenhelix.com to share your data in a secure fashion.

Please let me know how I can be of further assistance.

Thanks, Jami...

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answered 2014-06-09 08:44:06 -0600

Hello Jami,

I am having trouble loading VCF and BAM files we have in the lab that have been analyzed in the past. When I try to drag and drop them into the viewer, I get a stop sign.

Is there any annotation inside the file I need to check?

Thanks

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0

answered 2013-08-16 16:34:56 -0600

Hi Martin,

For a VCF file to be sorted the variants in the file must be listed one variant per line in ascending genomic order for the species.

Is GenomeBrowse giving an error message when you load the VCF file? Our importer is designed to handle well formed VCF files that are formatted based on specification determined by 1000Genomes.

What species and genome build is the data in the VCF file? Did a particular pipeline or software produce the VCF file?

If you would be willing to share a sample of the VCF data in a secure fashion please email me at genomebrowse@goldenhelix.com and I can provide details to upload the file to our secure server.

Please let me know how I can be of further assistance.

Thanks, Jami...

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answered 2013-08-16 07:22:56 -0600

Please elaborate when you state: "Currently any VCF file loaded into GenomeBrowse must be sorted". I received a VCF file which GenomeBrowse (recently downloaded) is not accepting and I'm not sure why.

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answered 2012-12-04 17:04:54 -0600

updated 2013-03-27 13:38:17 -0600

Hi Chelsea,

Thank you for your question. We are still in the process of developing and implementing the functionality to load VCF files directly into GenomeBrowse, unfortunately the target date of completion has been pushed to after the first of the year.

For the moment we recommend using our analysis software SVS to create custom annotation tracks from the data within the VCF files that can then be viewed within GenomeBrowse. SVS produces IDF files when creating custom tracks that will be auto-detected by GenomeBrowse.

SVS is Golden Helix’s analysis product for a variety of workflows and is a commercial tool, you can request an evaluation of the software from our evaluation request form.

Please feel free to use SVS in trial mode to curate your custom tracks for use with GenomeBrowse.

Thanks, Jami…

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Asked: 2012-12-04 12:21:43 -0600

Seen: 1,400 times

Last updated: Jun 10 '14