95208355e2c667d194b29ee78c8ca8a09c2c2596
max
  Fri Jul 17 08:51:28 2026 -0700
lrSv: add NIH CARD long-read SV subtrack (cardSv)

#Preview2 week - bugs introduced now will need a build patch to fix
Add the NIH CARD Long-Read Initiative structural-variant catalogue (351
post-mortem brain samples: 205 NABEC European ancestry, 146 HBCC
African/African-admixed) as a new subtrack of the Long-read SVs container.
The provider bigBed is re-derived into the shared lrSv schema: signed svLen
made positive (reference span), an explicit insLen added, the single
DUP:TANDEM folded to DUP, and colors remapped to the container's shared
svColor() palette. All 228,855 provider records are carried through 1:1.
Adds the converter and autoSql, the trackDb stanza with filters consistent
with the sibling subtracks, a full description page, a summary row and blurb
on the container page, and a makeDoc section. refs #36258

diff --git src/hg/makeDb/trackDb/human/lrSv.ra src/hg/makeDb/trackDb/human/lrSv.ra
index 69d5b38a81e..bfb4f3ba0be 100644
--- src/hg/makeDb/trackDb/human/lrSv.ra
+++ src/hg/makeDb/trackDb/human/lrSv.ra
@@ -501,30 +501,62 @@
     mouseOver <b>Var</b>: $name ($svType)<br><b>SV len</b>: $svLen<br><b>Ins len</b>: $insLen<br><b>Genes</b>: $geneCount
     filterValues.svType DEL,INS,DUP,INV,CPX
     filterType.svType multipleListOr
     filterLabel.svType SV Type
     filter.svLen 0:1321484
     filterByRange.svLen on
     filterLabel.svLen SV Length
     filter.insLen 0:31711
     filterByRange.insLen on
     filterLabel.insLen Insertion Length
     filter.geneCount 0:200
     filterByRange.geneCount on
     filterLabel.geneCount Gene Count
     skipEmptyFields on
 
+    track cardSv
+    parent longReadVariants
+    bigDataUrl /gbdb/$D/lrSv/card.bb
+    shortLabel CARD 351 SVs
+    longLabel Structural Variants from 351 Brain Samples (NIH CARD Long-read ONT, NABEC + HBCC)
+    type bigBed 9 +
+    itemRgb on
+    visibility hide
+    mouseOver <b>Var</b>: ${name} (${svType})<br><b>SV len</b>: ${svLen}<br><b>Ins len</b>: ${insLen}<br><b>AF</b>: ${alleleFreq}<br><b>Carriers</b>: ${AC} (NABEC ${nabecCount}, HBCC ${hbccCount})
+    filterValues.svType DEL,INS,INV,DUP
+    filterType.svType multipleListOr
+    filterLabel.svType SV Type
+    filter.svLen 0:30282742
+    filterByRange.svLen on
+    filterLabel.svLen SV Length
+    filter.insLen 0:92867161
+    filterByRange.insLen on
+    filterLabel.insLen Insertion Length
+    filter.AC 1:351
+    filterByRange.AC on
+    filterLabel.AC Carrier Count
+    filter.alleleFreq 0:1
+    filterByRange.alleleFreq on
+    filterLimits.alleleFreq 0:1
+    filterLabel.alleleFreq Allele Frequency
+    filter.nabecCount 0:205
+    filterByRange.nabecCount on
+    filterLabel.nabecCount NABEC Carriers (European ancestry)
+    filter.hbccCount 0:146
+    filterByRange.hbccCount on
+    filterLabel.hbccCount HBCC Carriers (African/African-admixed ancestry)
+
     # NOT FOR RELEASE: data received from Eichler lab via email, not yet published.
     # Do not add to lrSvAll merged track until a preprint or paper is available.
     track lrSv1kLin
     parent longReadVariants
     release alpha
     bigDataUrl /gbdb/$D/lrSv/lin1218.bb
     shortLabel 1KG Linear 1218 SVs
     longLabel Structural Variants from 1,218 Individuals (1000 Genomes, Linear Long-read)
     type bigBed 9 +
     itemRgb on
     visibility hide
     mouseOver <b>Var</b>: $name ($svType)<br><b>SV len</b>: $svLen<br><b>Ins len</b>: $insLen<br><b>AC</b>: $AC/$AN<br><b>AF</b>: $AF<br><b>AF (African)</b>: $afAfr<br><b>AF (European)</b>: $afEur<br><b>Samples</b>: $NS
     filterValues.svType DEL,INS
     filterType.svType multipleListOr
     filterLabel.svType SV Type