Add GeneticsLand Custom Query.pdf
From Array Suite Wiki
Users can add a "Custom Query" to stratify samples by genetic data content, and the resulting query can then applied, for example, to filter as as a grouping factor.
Add Omic Data Query
Select the Add Variant Data Query option, which is found to the direct right of Select View.
Once the query has been performed, the results will be displayed under the Sample Tab | Custom Query:
Sequenced or array based SNPs can be searched, depending on the land data content. Queries are position based. Users can search by rsID or by chr:position. Searches can be performed for 1 or multiple variants; however, each query is independent. For example, if multiple variants are used for data query, it is equal to multiple independent data queries.
1. Select to query Sequenced Data (i.e. VCF sequenced) or Genotyped Data (ie. VCF genotyped & PLINK format). Available data types are listed in the Query Control under Data Availability. An error will be returned if you attempt to query a variant with no data.
2. Select Input to bring up the menu option to Query Multiple Variants.
3. Opt to return exact genotypes or coded genotypes as AA/AB/BB, Hom reference/Het/Hom alternative, or 0-2 for alternative allele dose.
1. “Return AAmutation classification”: checking this box will perform specific query. For example, search for Y1666Y.
2. Choose the annotations to consider; details of variant annotation categories can be found at Variant Classification Guidelines.
3. Apply a filter to exclude based on 1000 genomes allele frequency.
Note: The ALL SNPs summary table view can be used to query land data for AA mutation, allele frequency, etc.
Delete Omic Data query
Users can delete a specific query or simply remove all queries.
Naming Custom Queries
By default, each query will contain the variant or gene name.
The user can also specify a custom label for the Query name. For each gene specified, the Query will be named GeneName Query name.