Publish lossless GRCh38 AVI SNV VCF mirror (September 8, 2026 release)

.gitattributes

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 # Video files - compressed
 *.mp4 filter=lfs diff=lfs merge=lfs -text
 *.webm filter=lfs diff=lfs merge=lfs -text
+avi.grch38.vcf.gz.tbi filter=lfs diff=lfs merge=lfs -text

README.md

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+---
+license: other
+license_name: alphagenome-services-additional-terms-of-service
+license_link: https://deepmind.google.com/science/alphagenome/terms
+pretty_name: AlphaGenome AVI GRCh38 — lossless indexed VCF mirror
+tags:
+  - genomics
+  - alphagenome
+  - variant-annotation
+  - grch38
+  - vcf
+  - biology
+size_categories:
+  - n>1B
+---
+
+# AlphaGenome AVI GRCh38 — prepared VCF mirror
+
+An unofficial, losslessly reformatted mirror of Google DeepMind's **AVI SNV
+scores**, prepared for [GUIDE-IEI](https://github.com/yimingluo-md/guide-iei).
+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](https://deepmind.google.com/science/alphagenome/downloads)
+- [Original AVI SNV ZIP](https://deepmind.google.com/science/alphagenome/_/download/atlas/avi_scores_snvs_tabix.zip)
+- [AlphaGenome Services Additional Terms of Service](https://deepmind.google.com/science/alphagenome/terms), last modified September 8, 2026
+- [AVI methodology](https://deepmind.google.com/science/alphagenome/learning#the-avi-model-and-scores)
+
+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:
+
+```vcf
+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:
+
+```bash
+tabix avi.grch38.vcf.gz 1:10001-10001
+```
+
+For Ensembl VEP, use an exact-allele custom VCF annotation:
+
+```text
+--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:
+
+```text
+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.

SOURCE_AND_TERMS.txt

@@ -0,0 +1,6 @@
+AlphaGenome AVI scores — Google DeepMind
+Source: https://deepmind.google.com/science/alphagenome/_/download/atlas/avi_scores_snvs_tabix.zip
+Terms: https://deepmind.google.com/science/alphagenome/terms
+Release: atlas-2026-09-08-vcf-v1
+Lossless per-position ALT grouping; Number=A raw/phred; chr prefix removed; no score rounding or filtering
+AVI is an impact prediction, not a clinical classification.

avi.grch38.vcf.gz

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+size 75764802676

avi.grch38.vcf.gz.tbi

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+size 2798486

manifest.json

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+{
+  "schema": "guide-iei.avi/v1",
+  "release": "atlas-2026-09-08-vcf-v1",
+  "assembly": "GRCh38",
+  "rows": 8812917339,
+  "positions": 2937639113,
+  "source": {
+    "url": "https://deepmind.google.com/science/alphagenome/_/download/atlas/avi_scores_snvs_tabix.zip",
+    "archive_sha256": "a237c198bc1c033da127fe0257129fdf246e7aa311f8fb584bb053ffa0c7966b",
+    "size": 88473344811,
+    "mtime_ns": 1788907637731062495,
+    "crc32": "6c6c1d44",
+    "converter_sha256": "c3629626f86820807aba7d2a8a79804a29805589ec2fcd992faa300021c18ba0"
+  },
+  "terms_url": "https://deepmind.google.com/science/alphagenome/terms",
+  "chromosomes": {
+    "1": 691443036,
+    "2": 721644684,
+    "3": 594300405,
+    "4": 569258001,
+    "5": 543796134,
+    "6": 510235566,
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+    "8": 434304408,
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+    "19": 175322274,
+    "20": 191832771,
+    "21": 120265857,
+    "22": 117479331,
+    "X": 464679087,
+    "Y": 79245129
+  },
+  "transformation": "Lossless per-position ALT grouping; Number=A raw/phred; chr prefix removed; no score rounding or filtering",
+  "converter_sha256": "c3629626f86820807aba7d2a8a79804a29805589ec2fcd992faa300021c18ba0",
+  "files": {
+    "avi.grch38.vcf.gz": {
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+      "sha256": "a34a9b48b6dbb3c769d86014e7f28062ef65420c5add7e88f30dfa50d5756b75"
+    },
+    "avi.grch38.vcf.gz.tbi": {
+      "size": 2798486,
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+      "sha256": "26d20b2855a478ec5b44bba8969a893453292bd432e6f969b01dd7a82334bbae"
+    }
+  }
+}