3dd0329ee0e804f5841a9998c4e7f024d3276921
lrnassar
  Wed Sep 9 17:20:20 2026 -0700
Releasing the AlphaGenome Variant Impact (AVI) score track for hg38. refs #38261

Moves the bigWigs to /gbdb/hg38/_alphaGenome/, the underscore convention that keeps
non-redistributable data off the download server, matching PromoterAI and PrimateAI,
and drops the alpha release tag.

Shortens the composite longLabel to fit the 85 character limit and lowercases Score
in the longLabels. Adds a New pennantIcon and points the Deleteriousness Predictions
container pennant at the Sept. 10 news post.

Corrects the median on the description page from 1.6 to 2.9. The old figure counted
the zero-filled reference base slots, which are not variants. Removes two threshold
statements that are not in the AlphaGenome Atlas preprint or any public source. Adds
the /gbdb symlink step to the makeDoc, and fixes three container page links that were
missing target=_blank.

diff --git src/hg/makeDb/doc/hg38/alphaGenome.txt src/hg/makeDb/doc/hg38/alphaGenome.txt
index 529b9bb9429..1a4a30e930e 100644
--- src/hg/makeDb/doc/hg38/alphaGenome.txt
+++ src/hg/makeDb/doc/hg38/alphaGenome.txt
@@ -1,57 +1,67 @@
 # AlphaGenome Variant Impact (AVI) score track, refs #38261
 # Fri Sep  4 14:20:00 PDT 2026 (Claude max)
 
 # Google DeepMind provided alphagenome_variant_impact_score_snvs.tsv.gz (83 GB, tabix
 # indexed) directly, along with terms.txt, their terms of service. The same data is on
 # https://deepmind.google.com/science/alphagenome/atlas
 # The file is a tab-separated table of chrom, pos, ref, alt, raw_score, PHRED covering
 # every possible single-base substitution in GRCh38. It holds no indels, despite what
 # the AlphaGenome Atlas offers, and no row where alt == ref.
 
 mkdir -p /hive/data/genomes/hg38/bed/alphaGenome
 cd /hive/data/genomes/hg38/bed/alphaGenome
 
 # We cannot redistribute this data, so the trackDb stanzas carry "tableBrowser off"
 # and the description page points users at Google for the download.
 
 # Split into one wig per alternate allele. The program copies the PHRED column through
 # as text, so no precision is lost, and it prints a full accounting of lines read,
 # lines skipped and values written. Took 28 minutes and 10.7 MB of memory.
 # Source: ~/kent/src/hg/oneShot/alphaGenomeToWig/alphaGenomeToWig.c
 alphaGenomeToWig alphagenome_variant_impact_score_snvs.tsv.gz
 
 # What it reported. Nothing was skipped: every input line became a score, and the
 # real scores written (values minus zero fills) equal the input line count exactly.
 #   read 8812917339 data lines, used 8812917339
 #     A: 2931187386 values in 399706 sections (860697142 zero fills)
 #     C: 2937603476 values in   3556 sections (599003079 zero fills)
 #     G: 2937603388 values in   3562 sections (601477231 zero fills)
 #     T: 2931143258 values in 402430 sections (863442717 zero fills)
 #   wrote 11737537508 values in 809254 sections, 2924620169 of them zero fills
 # 11737537508 - 2924620169 = 8812917339, matching the 8,812,917,339 data lines in
 # the input (wc -l minus the header). A and T have far more sections than C and G
 # because unscored stretches longer than maxGap fall more often between A/T scores.
 
 # On the number of fixedStep sections: because no row has alt == ref, each per-allele
 # file is missing roughly every fourth position. alphaGenomeToWig fills gaps of up to
 # -maxGap=10 bases with zero so one fixedStep block can span a long contiguous run.
 # Without this the file fragments into blocks of about 3.5 values each and the
 # resulting bigWig is roughly twice as large. Measured on 30 M lines of chr21:
 #   fixedStep wig  ->  34.5 MB bigWig
 #   bedGraph       ->  74.0 MB bigWig
 
 for n in A C G T; do
     wigToBigWig alphaGenome$n.wig ../../chrom.sizes $(echo $n | tr A-Z a-z).bw &
 done
 wait
 
 # Check the value range, this is what viewLimits/viewLimitsMax in trackDb are based on
 for n in a c g t; do bigWigInfo $n.bw | egrep "^(min|max|mean):"; done
 
 # Sanity check that the 1-based input maps to the right 0-based bigWig position.
 # chr21:5010001 G>A has PHRED 6.58432 in the source file:
 bigWigToBedGraph -chrom=chr21 -start=5010000 -end=5010004 a.bw stdout
 # chr21 5010000 5010001 6.58432   <- the G>A score
 # chr21 5010001 5010002 0         <- ref is A here, so no A>A row, zero filled
 
 # The wig files are only intermediates and can be deleted once the bigWigs check out.
+
+# Link the bigWigs into /gbdb. The directory name carries a leading underscore, which is
+# how we mark data that must not be copied to hgdownload: the admins' sync skips these
+# directories. The same convention is used by the PromoterAI and PrimateAI tracks, which
+# are also under Deleteriousness Predictions and also cannot be redistributed. The build
+# directory under /hive keeps its normal name; only the /gbdb path is underscored.
+mkdir -p /gbdb/hg38/_alphaGenome
+for n in a c g t; do
+    ln -sf /hive/data/genomes/hg38/bed/alphaGenome/$n.bw /gbdb/hg38/_alphaGenome/$n.bw
+done