This is actually multiple fields - one for each ancestry determination.įor example, one field would be gvs_afr_ac. The max is calculated in the same way as max AN, max AC, etc. This is actually multiple fields - one for each of the eight gnomad subpopulations (see above).Īll of Us subpopulations can be found in Table 2.Īll of Us: Max subpopulation allele count.Īll of Us: Max subpopulation allele number. This is actually multiple fields - one for each of the eight gnomad subpopulations. To calculate the max subpopulation, see Appendix A. Gnomad subpopulations can be found in Table 2. Primary Transcript ID (see canonical description in NIRVANA) nomenclature DNA change in transcript space. This should only happen when transcript is null. Null value indicates that the variant is in an IGR. See FAQ #1 for more info on the relationship between transcripts, genes, and variants. Note that transcript to gene is still one-to-one, so this field is a single gene symbol. A variant can have more than one associated gene symbol, since about 3% of genes do overlap.
Sample count of heterozygous plus homozygous alternate genotypes.įor rules on calculating this field, please see Appendix B. More than one base for insertions.Īlternate allele count across all available samples in the WGS joint callset.Īllele number across all available samples in the WGS joint callset.Īlternate allele frequency (AC/AN) across all available samples in the WGS joint callset. This should always be one base for SNPs and deletions. More than one base for deletions.īase(s). This should always be one base for SNPs and insertions. Must be positive exact position for a SNP and the position before the alteration in an indel.īase(s). the variant is in an intergenic region (IGR)) Null indicates that this variant does not overlap any transcripts (i.e. Note that a variant cannot have multiple alternate alleles - only one. Unique string for identifying a variant (as produced by NIRVANA based on a spec from Broad Institute). For the exact locations of these files, please see the Controlled CDR Directory. A code snippet is provided in the featured notebook 01_Get Started with Genomic Data. In other words, one site can have multiple variants in a VCF. Table 1 details the fields in the VAT.Ī variant is not a 1:1 correspondence to the genomic sites represented in a Variant Calling Format (VCF) file, since a single row in a VCF (“site”) can be multi-allelic.
Therefore, allele counts (fields: gvs_*_ac) and allele numbers (fields: gvs_*_an) of zero are possible. Please note that all of the All of Us population annotations exclude filtered genotypes (FT tag populated with a non-missing or “PASS” value). The remaining annotations are the All of Us population metrics (fields: gvs_*), which we generate internally.
We generate most of the functional annotations using NIRVANA 3.18, a functional annotation tool from Illumina that provides annotations of genomic variants based on the Sequence Ontology consequences and external data sources for additional context (ex. The variants are called against the hg38/GRCh38 reference a detailed description about the variant calling analysis is in the Genomic Research Data Quality Report All of Us Genomic QC Report. However, each variant can overlap multiple transcripts and thus have multiple records, representing different variant transcript combinations. Each row represents a variant-transcript combination and there is only one record per variant transcript combination. The VAT includes annotations like the gene symbol and protein change, delivered as a block compressed tab-separated value text file (.tsv.bgz), which can be loaded into Hail. Sites with 50 or more alternate alleles are not included in the VAT. Functional annotations for passing variants in the short read whole genome sequencing (srWGS) SNP and Indel dataset are available in the Variant Annotation Table (VAT).