78cdae7249c8609dcbc743e996ea7e5eec33d75a
max
  Mon Aug 17 08:15:39 2026 -0700
lrSv: fix off-by-one anchor base in deletion coordinates across converters, refs #38099

VCF/pangenome deletions carry a non-deleted anchor (padding) base at POS.
Several lrSv converters set chromStart = pos-1, which includes that anchor, so
each deletion was 1 bp too wide on the left and svLen was 1 too big. Callsets
handled this inconsistently, so the same deletion appeared at offset coordinates
and failed to merge in lrSvAll.

For deletions only (INS/INV/CPX unchanged), advance chromStart past the anchor
so the interval covers exactly the deleted bases (svLen == |SVLEN|). Verified
against the hg38 reference: the old left base is present in both REF and ALT
(i.e. retained by the sample), so it should not be inside the deletion.

Fixed 11 converters: lrSv1kLin1218VcfToBed, lrSv1kgOntVcfToBed,
lrSvGustafsonVcfToBed, lrSvGa4kSvVcfToBed, lrSvDecodeVcfToBed,
lrSvAou1kCsvToBed, lrSvColorsDbSvVcfToBed, lrSvCardBbToBed, lrSvAprVcfToBed,
lrSvCpc1VcfToBed, lrSvVcfToBed (generic, used by han945).

Left unchanged, verified already anchor-correct: hgsvc3 and hgsvc2 (0-based
source), hprc2v21 (Ro converter prefix-trims), noyvert/tommoJp (POS is the
first deleted base), chirmade101 (1-based-closed source).

Rebuilt all affected bigBeds (hg38 + hs1 where present) and the lrSvAll merge:
3,111,026 -> 2,963,093 rows as ~148k duplicate deletions now merge.

diff --git src/hg/makeDb/scripts/lrSv/lrSv1kgOntVcfToBed.py src/hg/makeDb/scripts/lrSv/lrSv1kgOntVcfToBed.py
index cb2cfe65186..0ad6e60fc8a 100644
--- src/hg/makeDb/scripts/lrSv/lrSv1kgOntVcfToBed.py
+++ src/hg/makeDb/scripts/lrSv/lrSv1kgOntVcfToBed.py
@@ -89,30 +89,36 @@
                 continue
 
             fields = line.rstrip("\n").split("\t")
             chrom = fields[0]
             pos = int(fields[1])
             varId = fields[2]
             ref = fields[3]
             info = parseInfo(fields[7])
 
             svTypeRaw = getSvClass(varId)
             svType = normalizeSvType(svTypeRaw)
 
             # BED coordinates: 0-based half-open
             chromStart = pos - 1
             chromEnd = chromStart + len(ref)
+            # VCF POS is the anchor base (in REF and ALT); it is not part of a
+            # deletion, so drop it from the left of DEL intervals. chromEnd
+            # already points one past the last deleted base, so only chromStart
+            # moves. INS keeps the anchor-based position.
+            if svType == "DEL":
+                chromStart += 1
 
             # Source lengths: INS_LEN for insertion size, DEL_LEN for deletion size
             insLenSrc = int(info.get("INS_LEN", "0"))
             delLenSrc = int(info.get("DEL_LEN", "0"))
 
             # For INS, the item spans only the anchor base; expand by 1 for visibility
             if svType == "INS" and chromEnd <= chromStart + 1:
                 chromEnd = chromStart + 1
 
             # svLen = span on reference
             svLen = chromEnd - chromStart
             # insLen = length of inserted sequence (INS only); 0 otherwise
             if svType == "INS":
                 insLen = insLenSrc
             elif svType == "DEL":