Gene.VcfSnp.CarrierSampleDetails

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Carrier Sample Details

CarrierSampleDetails.jpg

Contents


Overview

This table view provides an un-pivoted list of coding genotype with both sample attributes and variant annotations.

This View is available in the single gene search context, in the Sequenced section in Select View:

CarrierSampleDetailsSelect.jpg

Data/Metadata Requirements

Since this an un-pivoted (tall-skinny) list of genotypes, it can easily become very large and impractical (number of rows will be the product of sample count and variant count). To keep the row count to a reasonable size, it will be filtered to rare coding variants by default using the cross-population frequency as reported by gnomAD to define rareness: CarrierSampleDetailsGnomAD.jpg

Please ensure your GeneticsLand has the gnomAD classifier specified.

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Implicit pre-processing

In addition to pre-filtering to rare variants, it will also be filtered to coding variants. Specifically, those predicted based on the gene model: CarrierSampleDetailsCoding.jpg

Customizing This View

CarrierSampleDetailsSelectColumns.jpg

  • Specify Columns: By default, this table will include additional columns with the sample attributes (i.e. those visible in the Land's Sample Details table view) and variant annotations. Depending on the metadata content (sample attributes) and variant classifier configuration, this could be many columns so you may wish to specify only a subset of these which are of interest to display.

Filtering

As this view is designed to display carrier status of functional variants, you may wish to further filter on additional variant annotations (e.g. SIFT) to narrow in on those most likely to have a biological effect: CarrierSampleDetailsSIFT.jpg

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