I'm very new to the platform and I'm trying to look at variations of the APOE gene, so I'm trying to input things like rs429358(C;T), rs7412(C;C) to specify versions of this gene in the cohort browser - however this is not working. Is there a better way to browse by APOE gene status or to input the rs as above? Thanks for any help!
These tables contain limited information about alleles and genotypes, transcribed into SQL from the pVCF files of Data-field 23146 and/or 23148 and/or 23157 (along with added annotations). These tables are used by the Cohort Browser in the creation of the "GENOMICS" tab. They have not been optimized for direct SQL querying, and their schema and conventions are subject to change. For this reason, it is not recommended to access these tables on your own but to access the bulk files instead.
Within the genomics tab of the cohort browser, if you search for the rsid and scroll down to the allele table, you can see which is the ref and which is the alt. You can then Add Filter to Filter the participants by Variant, either selecting Homozygous Alt or Heterozygous Alt,
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HI {@00582000000IgZIAA0}?,
I think that querying by this specific format is not possible in CB. In Geno tab, you can input rsid and you should get all alleles for this rsid.
What I would try is to build a Spark SQL query in Spark based JupyterLab, you can attempt to query (though it is not optimized) tables "allele" and "genotype", as it is mentioned here: https://dnanexus.gitbook.io/uk-biobank-rap/working-on-the-research-analysis-platform/using-spark-to-analyze-tabular-data#accessing-the-database-directly-using-sql
If your access application has been approved for Data-field 23146, 23148, and/or 23157 you will also see the following tables:
Allele_23146, allele_23148, allele_23157, annotation_23146, annotation_23148, annotation_23157, assay_eid_map_23146, assay_eid_map_23148, assay_eid_map_23157, genotype_23146, genotype_23148, genotype_23157, pheno_assay_23146_link, rsid_lookup_r81_23146, pheno_assay_23146_link, rsid_lookup_r81_23148, pheno_assay_23157_link, and rsid_lookup_r81_23157.
These tables contain limited information about alleles and genotypes, transcribed into SQL from the pVCF files of Data-field 23146 and/or 23148 and/or 23157 (along with added annotations). These tables are used by the Cohort Browser in the creation of the "GENOMICS" tab. They have not been optimized for direct SQL querying, and their schema and conventions are subject to change. For this reason, it is not recommended to access these tables on your own but to access the bulk files instead.
Within the genomics tab of the cohort browser, if you search for the rsid and scroll down to the allele table, you can see which is the ref and which is the alt. You can then Add Filter to Filter the participants by Variant, either selecting Homozygous Alt or Heterozygous Alt,
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