VcfData

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VCF Data (Table)

VcfData.png

Contents


Overview

This provides a streaming view of all VCF (Sequenced) files published to the GeneticsLand.

This View is available in the main GeneticsLand context, in the File Management section in Select View:

FileMgmtVcfData.png

This view is designed to provide visibility of additional details not stored in GeneticsLand. Only genotypes are stored in GeneticsLand so when browsing the Land or querying for export, only the genotypes will be available. This view provides access to the original source VCF file including the variant and genotype attributes which are not stored in GeneticsLand (select a row to view the detailed genotype attributes below)

VcfDataAttrib.png

Filtering variants (rows)

After selecting which file to stream and waiting for the VCF view to open, switch to the Filter tab on the left where you can filter on the ID column or using coordinates:

VcfDataFilter.png

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Filtering samples (columns)

To filter to a particular sample(s), switch to the Task tab on the right and select Specify Columns to manage which columns are displayed:

VcfDataSpecCol.png

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Access controls

Access to this steaming view of the source file is not controlled by the Project-level access controls in the Land. Instead, there are file-level access controls which the user who published the file can manage (as well as administrators). After selecting which file to stream and waiting for the VCF view to open, click on the Update Current Table icon on the left where you can manage which groups have read and edit access after un-ticking the Private table box.

VcfDataAccess.png

Note, granting access to a group through this mechanism is sufficient to make the file viewable in this context regardless of the user's access to the folder where the file is located.

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