5e4ca58df1b5bfe554fe5cc3309a39736ca256ee
max
  Tue Apr 21 08:08:52 2026 -0700
cpc1Sv: restrict to the 58 CPC samples, drop HPRC-specific SVs

Rewrite lrSvCpc1VcfToBed.py to identify the 58 CPC sample columns by
name prefix (HIFI032* or RY*), recompute AC/AN/NS from those GT
columns only, and skip any snarl that no CPC sample carries. The
HPRC portion is already represented elsewhere in lrSv, so this keeps
the track population-consistent with its label.

Rebuild results: 46,092 snarl sites on hs1 (down from 97,205 when
combined with HPRC), 36,030 lifted to hg38 (down from 81,261;
10,062 unmapped). Updates cpc1Sv.html, lrSv.ra labels, and the
makeDoc.

refs #36258

diff --git src/hg/makeDb/trackDb/human/lrSv.ra src/hg/makeDb/trackDb/human/lrSv.ra
index 39431a27917..2fb6a445a4e 100644
--- src/hg/makeDb/trackDb/human/lrSv.ra
+++ src/hg/makeDb/trackDb/human/lrSv.ra
@@ -1,30 +1,31 @@
 track lrSv
 superTrack on
 shortLabel Long-read SVs
 longLabel Structural Variants from Long-read Sequencing
 group varRep
 visibility hide
 
     track colorsDbSv
     parent lrSv
     bigDataUrl /gbdb/$D/lrSv/colorsDb/sv.$D.bb
     shortLabel CoLoRSdb 1,427 SVs
     longLabel Structural Variants from CoLoRSdb (Consortium of Long-Read Sequencing, 1,427 Samples)
     type bigBed 9 +
     itemRgb on
     visibility dense
+    dataVersion v1.2.0
     mouseOver <b>$name</b> ($svType) len=$svLen AF=$af AC=$AC (Hom:$AC_Hom Het:$AC_Het Hemi:$AC_Hemi) samples=$NS
     searchIndex name
     filterValues.svType DEL,INS,INV
     filterType.svType multipleListOr
     filterLabel.svType SV Type
     filter.svLen 20:101381
     filterByRange.svLen on
     filterLabel.svLen SV Length
     filter.AC 0:2854
     filterByRange.AC on
     filterLabel.AC Alt Allele Count (AC)
     skipEmptyFields on
     priority 1
 
     track lrSv1kgOnt
@@ -397,32 +398,32 @@
     filterValues.svType INS,DEL,CPX,MIXED
     filterType.svType multipleListOr
     filterLabel.svType SV Type
     filterByRange.svLen on
     filterLabel.svLen SV Length
     filterByRange.alleleFreq on
     filterLimits.alleleFreq 0:1
     filterLabel.alleleFreq Allele Frequency
     filterByRange.alleleCount on
     filterLabel.alleleCount Allele Count
     skipEmptyFields on
 
     track cpc1Sv
     parent lrSv
     bigDataUrl /gbdb/$D/lrSv/cpc1.bb
-    shortLabel CPC+HPRC 105 SVs
-    longLabel Structural Variants from CPC + HPRC Phase 1 Pangenome (105 samples, 58 Chinese + 47 HPRC)
+    shortLabel CPC 58 SVs
+    longLabel Structural Variants from Chinese Pangenome Consortium (58 samples, CPC portion of the CPC+HPRC graph; HPRC-specific SVs removed)
     type bigBed 9 +
     itemRgb on
     visibility dense
     mouseOver <b>$name</b> ($svType) len=$svLen AC=$alleleCount/$alleleNumber AF=$alleleFreq samples=$numSamples alts=$numAlts
     filterValues.svType INS,DEL,CPX,MIXED
     filterType.svType multipleListOr
     filterLabel.svType SV Type
     filterByRange.svLen on
     filterLabel.svLen SV Length
     filterByRange.alleleFreq on
     filterLimits.alleleFreq 0:1
     filterLabel.alleleFreq Allele Frequency
     filterByRange.alleleCount on
     filterLabel.alleleCount Allele Count
     skipEmptyFields on