luoyiming1991/alphagenome-avi-grch38

AlphaGenome AVI GRCh38 — prepared VCF mirror

An unofficial, losslessly reformatted mirror of Google DeepMind's AVI SNV scores, prepared for GUIDE-IEI, and can be used directly for Ensembl VEP custom annotation. Google DeepMind produced the predictions; GUIDE-IEI performed only the format conversion described below. This mirror is not affiliated with or endorsed by Google DeepMind.

Source and terms

• Official AlphaGenome downloads
• Original AVI SNV ZIP
• AlphaGenome Services Additional Terms of Service, last modified September 8, 2026
• AVI methodology

The official downloads page lists AVI SNV scores in its permissive-use category for commercial and non-commercial use. This is subject to the applicable AlphaGenome terms, not a public-domain or Creative Commons release. Review those terms directly for the permissions, exceptions and restrictions that apply to your use. This mirror grants no additional rights and does not change the upstream terms. It contains only AVI raw and Phred scores—not the separately governed AVI feature breakdown, other Atlas predictions, model weights, or API credentials.

Scores are computational predictions, not clinical pathogenicity classifications. No clinical-use authorization or diagnostic validation is claimed by this mirror. Cite and attribute the original AlphaGenome work as specified by the upstream project; also identify this format conversion when needed for reproducibility.

Contents

Release: atlas-2026-09-08-vcf-v1.

File	Size (bytes)	Purpose
avi.grch38.vcf.gz	75,764,802,676	BGZF VCF containing all scores
avi.grch38.vcf.gz.tbi	2,798,486	Tabix VCF index
manifest.json	Small JSON	Source identity, counts, transformation and SHA-256 checksums
SOURCE_AND_TERMS.txt	Small text	Attribution and upstream links

There are 8,812,917,339 scored SNV alleles, grouped into 2,937,639,113 VCF records. Coverage is GRCh38 chromosomes 1–22, X and Y. Mitochondrial and alternate contigs and indels are not included. These are reference predictions for possible alleles; the VCF contains no patient samples or genotypes.

Exact transformation

The original BGZF TSV columns are #CHROM, POS, REF, ALT, raw_score and PHRED. For every position, the three possible alternate nucleotides are grouped into one VCF record. ALT order is A,C,G,T excluding REF. Both INFO fields are declared Number=A, Type=Float, so each value corresponds to the ALT in the same slot:

1	10001	.	T	A,C,G	.	.	raw=-0.03868,-0.032,-0.0372;phred=1.06466,1.3114,1.11839

The chromosome chr prefix was removed. Coordinates remain 1-based GRCh38. Score decimal text is unchanged: no rounding, imputation, thresholding, filtering or liftover was performed. Negative raw values and zero are retained. No gene or transcript assignment was added.

raw is the upstream AVI raw score; phred is the upstream Phred-scaled score. A high impact score is not itself a clinical P/LP classification. Missing coverage is not evidence of benignity.

Using the files

Download the VCF and its .tbi together, preserving their names. Do not recompress the VCF with ordinary gzip or use the index with a different file. Standard Tabix queries work:

tabix avi.grch38.vcf.gz 1:10001-10001

For Ensembl VEP, use an exact-allele custom VCF annotation:

--custom file=/path/avi.grch38.vcf.gz,short_name=AlphaGenomeAVI,format=vcf,type=exact,coords=0,fields=raw%phred

This produces AlphaGenomeAVI_raw and AlphaGenomeAVI_phred, including on intergenic consequences. Match chromosome, position, REF and ALT, not position alone. Select the matching ALT's score; do not take a maximum over the three alternate alleles or interpret the list as three independent models.

Integrity and provenance

The preparation checked the source schema and index, BGZF decompression CRCs, sorted positions, finite scores, nonnegative Phred values, three distinct alternate nucleotides at each position, and chromosome/total row counts. The completed VCF was indexed with Tabix. VEP integration tests verified reversed ALT ordering, intergenic annotations and rejection of a mismatched REF allele.

SHA-256:

a34a9b48b6dbb3c769d86014e7f28062ef65420c5add7e88f30dfa50d5756b75  avi.grch38.vcf.gz
26d20b2855a478ec5b44bba8969a893453292bd432e6f969b01dd7a82334bbae  avi.grch38.vcf.gz.tbi

The original source ZIP's SHA-256 is a237c198bc1c033da127fe0257129fdf246e7aa311f8fb584bb053ffa0c7966b. The manifest records the converter source SHA-256 and per-chromosome allele counts. Original modification timestamps in the manifest are provenance, not expected filesystem timestamps after downloading from this mirror.