Variant Search within the Cohort Builder

  • Updated

To construct your cohort based on genomic data, you can use our point and click tools to include participants in your cohort with genomic data of interest. Using the Cohort Builder "variant search" feature, you can filter by Gene, Consequence, ClinVar Significance Filter, Allele Count, Allele Number and Allele Frequency and sort by participant count, as well as add all participants with structural variants to your cohort inclusion criteria.

Please note: using this feature sets the query parameters to identify applicable person ids based on the inclusion and exclusion criteria you select within the tool. It will not extract the genomic data, but will help set the cohort parameters. To access genomic data for your cohort you will need to follow the extraction process directly in your notebook, or using our genomic extraction tool. See these support materials to learn more: Selecting Genomic data: using the Genomic Extraction tool; How to Work with All of Us Genomic Data (Hail - Plink) (Researcher Workbench login required). The extraction process described using the Genomic Extraction tool should only be used when you want to analyze Whole Genome Sequencing (WGS) data in a smaller subset of participants (less than 5,000 participants). This process will not work for array genomic data. For larger cohorts, you'll need to pull data directly into a notebook using files in the Controlled CDR Directory.

 

To select all participants with Structural Variant data

1. Build your cohort using Cohort Builder under the "Data" tab of your workspace

2. Select "Add Criteria" > "Structural Variant Data"

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To select participants with SNP/Indel Variants

1. Build your cohort using Cohort Builder under the "Data" tab of your workspace

2. Select "Add Criteria" > "SNP/Indel Variants"

3. Search for your variant of interest by typing the gene, variant, RS number or genomic region

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4. To filter search, select "Filter & Sort" - applying this tool shows results filtered by Gene, Consequence, ClinVar Significance Filter, Allele Count, Allele Number and Allele Frequency or sorted according to various options such as participant count or variant ID. 

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5. Select your variant of interest and save criteria.

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6. When all inclusion and exclusion criteria are added for your cohort select "Create Cohort." This cohort can then be used to create a dataset via Dataset Builder. To learn how to use the genomics extraction tool for our short read WGS genomics data, please see this support article here: Selecting Genomic data: using the Genomic Extraction tool. 

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To learn more about working with genomic data, please see these support articles -Accessing Genomic Data in the All of Us Controlled Tier, Controlled CDR Directory, Working with Genomic Data, How do I select specific variants from the Hail MatrixTables or Hail VDS?

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