What reference are the variants called against for the genomic data?

The array and short read whole genome sequencing (srWGS) variants are called against the hg38/GRCh38 reference. Below are locations of the public reference and auxiliary files:

• FASTA: gs://genomics-public-data/references/hg38/v0/Homo_sapiens_assembly38.fasta
• FAI: gs://genomics-public-data/references/hg38/v0/Homo_sapiens_assembly38.fasta.fai
• DICT: gs://genomics-public-data/references/hg38/v0/Homo_sapiens_assembly38.dict

The long read whole genome sequencing (lrWGS) variants are called against two references. grch38_noalt corresponds to the GRCh38 reference with no alternate sequences. T2Tv2.0 corresponds to the T2T-CHM13v2.0 reference, with the EBV contig added from the grch28_noalt reference.

For more detailed information regarding the the genomic data, we recommend the following articles:

1. How the All of Us Genomic data are organized
2. All of Us Genomic Quality Report