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VCF file support

asked 2012-09-27 11:12:55 -0600

Alex Stoddard gravatar image

Can GenomeBrowse load .vcf files?

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answered 2013-03-27 09:29:14 -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 2012-09-27 11:16:46 -0600

GenomeBrowse does not currently support VCF file format. However, we are working on implementing a tool in GenomeBrowse that will allow for direct VCF visualization as a sample-based variant plot. We have it schedule for release by the beginning of November 2012.

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Asked: 2012-09-27 11:12:55 -0600

Seen: 10,253 times

Last updated: Mar 27 '13