The All of Us Researcher Workbench team released a hotfix to the All of Us v7 Variant Annotation Table (VAT) on November 9, 2023 to ensure consistency with the allele number (gvs_*_an) and allele fraction (gvs_*_af) values.
As a result of the hotfix, the VAT was updated to address impacted allele number (gvs_*_an) and allele fraction (gvs_*_af) values.
Our team found that allele number (gvs_*_an) and allele fraction (gvs_*_af) values were inflated for records near the beginning of chromosome calling regions. We recommend that researchers use the updated VAT for any future analysis. For any previously completed analysis, we have described in the following section how to determine which variants were affected.
This upgrade only affects researchers who are using the gvs_*_an and gvs_*_af in the VAT.
Background
The VAT was updated to correct for an issue that resulted in some positions of the genome having variants with an inflated allele number (gvs_*_an) and allele fraction (gvs_*_af) fields. These incorrect values are a result from variants at the beginning of chromosome calling regions called as erroneous homref genotypes (GT = 0/0), instead of no calls (GT = ./.).
The affected variants are all at the beginning of chromosomes, which was the beginning of the regions we used for variant calling. Less than 0.03% of variants on the autosome and chromosome X were affected. On chromosome Y, 4.10% of the variants were impacted. On the autosome, the allele number count was not inflated by a high percentage. Less than 0.004% of the variants had an allele number error greater than 1%.
If you use any of the gvs_*_an or gvs_*_af fields in your analyses, we recommend that you upgrade to the new version of the VAT and re-run any completed analyses.
File Path Updates
We updated the Controlled CDR Directory page on the User Support Hub to include the new VAT locations. Table 1 contains a summary of the original, new, and deprecated VAT locations:
Table 1: Original, new, and deprecated locations for the VAT
| Status | Location |
| Original | gs://fc-aou-datasets-controlled/v7/wgs/short_read/snpindel/aux/vat/vat_complete.bgz.tsv.gz |
| New | gs://fc-aou-datasets-controlled/v7/wgs/short_read/snpindel/aux/vat/vat_complete_v7.1.bgz.tsv.gz |
| Deprecated | gs://fc-aou-datasets-controlled/v7/wgs/short_read/snpindel/aux/vat/vat_complete_deprecated.bgz.tsv.gz |
If you cannot upgrade immediately, we recommend that you use the deprecated location (Table 1) until you are able to update to the new location. Note: You will need to transition to the new location within 60 days (by 3/8/24).
If you have any questions regarding the hotfix, please contact us at support@researchallofus.org.
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