8e053a77fec3df57d9bfa44fafbb07c0cdadd1a7
max
  Fri Sep 4 15:47:07 2026 -0700
AlphaGenome Variant Impact (AVI) score track for hg38

New track under the Deleteriousness Predictions container showing Google
DeepMind's AlphaGenome Variant Impact score for every possible single-base
substitution, as four bigWigs, one per alternate allele.

alphaGenomeToWig splits the 83 GB source table into one fixedStep wig per
alternate allele. It copies the PHRED column through as text so no precision
is lost, and zero-fills gaps up to -maxGap so a fixedStep block can span a
long contiguous run. The input has no row where alt == ref, so each per-allele
file is missing roughly every fourth position; without the fill the wig
fragments into blocks of about 3.5 values and the bigWig doubles in size.
All 8,812,917,339 input lines were used, none skipped.

The data cannot be redistributed, so the stanzas set tableBrowser off and the
description page sends users to the AlphaGenome Atlas. Alpha only for now.
No reference yet, the score is unpublished.

refs #38261

diff --git src/hg/oneShot/alphaGenomeToWig/makefile src/hg/oneShot/alphaGenomeToWig/makefile
new file mode 100644
index 00000000000..29ce3a0b6ca
--- /dev/null
+++ src/hg/oneShot/alphaGenomeToWig/makefile
@@ -0,0 +1,19 @@
+kentSrc = ../../..
+include ../../../inc/common.mk
+
+L += -lm
+MYLIBDIR = ../../../lib/${MACHTYPE}
+MYLIBS = ${MYLIBDIR}/jkweb.a
+
+A = alphaGenomeToWig
+O = alphaGenomeToWig.o
+
+${A}: ${O} ${MYLIBS}
+	${CC} ${COPT} -o ${DESTDIR}${BINDIR}/${A}${EXE} ${O} ${MYLIBS} $L
+	${STRIP} ${DESTDIR}${BINDIR}/${A}${EXE}
+
+compile:: ${O}
+	${CC} ${COPT} -o ${A}${EXE} ${O} ${MYLIBS} $L
+
+clean::
+	rm -f ${A}${EXE} ${O}