Cohort browser for Genomics
What type of genomics data are we filtering in the cohort browser? Is it whole genome sequencing data or exome sequencing..?
What type of genomics data are we filtering in the cohort browser? Is it whole genome sequencing data or exome sequencing..?
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The cohort browser in the RAP is using the UKB Whole Exome Sequencing data.
There is an allele frequency browser based on the UKB Whole Genome Sequencing at https://afb.ukbiobank.ac.uk/ , which is publicly available.
The genomics search in Showcase is using the genotyping data, in GRCh37 coordinates. (WES and WGS are in GRCh38)
Is there anyway to create a cohort using the allele frequency browser?
No, that is not possible.
What do you recommend as the best way to search for specific variants? I searched for variants on the cohort browser in the RAP which is using the UKB Whole Exome Sequencing data and no variants were found. When I searched the public allele frequency browser based on the UKB Whole Genome Sequencing data at https://afb.ukbiobank.ac.uk/ I found some of the variants I was looking for. What is the best way to find these variants from the RAP WGS data so that I can pull these subjects' IDs out to look at their phenotypic data?
There are pVCFs (population VCFs) available for all 500K participants (see https://biobank.ctsu.ox.ac.uk/showcase/label.cgi?id=180). Common filtering tools (bcftools, plink) are available as part of the dx swiss-army-knife toolkit (https://dnanexus.gitbook.io/uk-biobank-rap/working-on-the-research-analysis-platform/tools-library). The pVCFs are divided into sequential blocks of 20kb.
We are aiming to release the files in PLINK2 and bgen later in the year.
Are there resources for assisting in using plink or bcftools? Like command line guides or entries that can be copied?
This resource may be helpful: https://github.com/UK-Biobank/UKB-RAP-Notebooks, particularly notebook 107: Merging, converting and filtering variant data using PLINK.
See also the repo provided by DNAnexus https://github.com/dnanexus/UKB_RAP
Showcase Resource 2009 contains genomic ranges for individual DRAGEN WGS pVCF block files 500k release
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