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
@@ -43,15 +43,25 @@
 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