06a482a2120d4d85c7c34fb5038213e07f595554
max
  Tue Apr 21 15:00:21 2026 -0700
lrSv: add tommoJpCnv short-read CNV comparator (multiWig)

ToMMo 48KJPN-CNV Frequency Panel: copy-number variation frequencies
from short-read whole-genome sequencing of 48,874 Japanese individuals
(jMorp 20230828 release, GATK CNV germline workflow at 1 kb
resolution). Published as a companion short-read comparator to the
long-read tommoJpSv track.

Rendered as a multiWig container with two bigWig subtracks (transparent
overlay): tommoJpCnvLoss.bw counts samples at CN<2 per bin (red) and
tommoJpCnvGain.bw counts samples at CN>2 per bin (green). Values are
absolute carrier counts out of 48,874. 2,006,905 bins with at least one
CNV carrier; bins that are wholly CN=2 are omitted.

Files:
- trackDb/human/lrSv.ra: new tommoJpCnv multiWig container
- trackDb/human/tommoJpCnv.html: new doc page
- trackDb/human/lrSv.html: summary-table row + per-track blurb
- scripts/lrSv/lrSvTommoJpCnvVcfToBedGraph.py: VCF -> two bedGraphs
- doc/hg38/lrSv.txt: wget, converter invocation, bigWig build steps

refs #36258

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

diff --git src/hg/makeDb/trackDb/human/lrSv.ra src/hg/makeDb/trackDb/human/lrSv.ra
index 2fb6a445a4e..ca027b343a1 100644
--- src/hg/makeDb/trackDb/human/lrSv.ra
+++ src/hg/makeDb/trackDb/human/lrSv.ra
@@ -191,30 +191,63 @@
     filterType.svType multipleListOr
     filterLabel.svType SV Type
     filter.svLen 0:99743
     filterByRange.svLen on
     filterLabel.svLen SV Length
     filter.sampleCount 1:945
     filterByRange.sampleCount on
     filterLabel.sampleCount Number of Supporting Samples
     filter.alleleFreq 0:1
     filterByRange.alleleFreq on
     filterLimits.alleleFreq 0:1
     filterLabel.alleleFreq Allele Frequency
     skipEmptyFields on
     urls chr2="hgTracks?position=$$"
 
+    track tommoJpCnv
+    parent lrSv
+    container multiWig
+    aggregate transparentOverlay
+    showSubtrackColorOnUi on
+    shortLabel ToMMo 48K CNV SR
+    longLabel CNV Carrier Counts from 48,874 Japanese Individuals (ToMMo 48KJPN-CNV, short-read WGS; 1 kb bins) - included for comparison
+    type bigWig 0 48874
+    autoScale on
+    viewLimits 0:1000
+    viewLimitsMax 0:48874
+    maxHeightPixels 100:32:8
+    visibility full
+    priority 2.5
+
+        track tommoJpCnvLoss
+        parent tommoJpCnv
+        bigDataUrl /gbdb/$D/lrSv/tommoJpCnvLoss.bw
+        shortLabel ToMMo CNV Loss
+        longLabel Samples with copy-number loss (CN<2) per 1 kb bin, ToMMo 48KJPN-CNV
+        type bigWig 0 48874
+        color 200,0,0
+        altColor 200,0,0
+
+        track tommoJpCnvGain
+        parent tommoJpCnv
+        bigDataUrl /gbdb/$D/lrSv/tommoJpCnvGain.bw
+        shortLabel ToMMo CNV Gain
+        longLabel Samples with copy-number gain (CN>2) per 1 kb bin, ToMMo 48KJPN-CNV
+        type bigWig 0 48874
+        color 0,160,0
+        altColor 0,160,0
+
     track tommoJpSv
     parent lrSv
     bigDataUrl /gbdb/$D/lrSv/tommoJp.bb
     shortLabel ToMMo Japanese SVs
     longLabel Structural Variants from 333 Japanese Individuals (ToMMo, 111 Trios)
     type bigBed 9 +
     itemRgb on
     visibility dense
     mouseOver <b>$name</b> ($svType) len=$svLen AF=$alleleFreq AC=$alleleCount
     filterValues.svType DEL,INS
     filterType.svType multipleListOr
     filterLabel.svType SV Type
     filter.svLen 51:99980
     filterByRange.svLen on
     filterLabel.svLen SV Length