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/lrSvVcfToBed.py src/hg/makeDb/scripts/lrSv/lrSvVcfToBed.py
index 6c48315c4d2..65eb708f1af 100644
--- src/hg/makeDb/scripts/lrSv/lrSvVcfToBed.py
+++ src/hg/makeDb/scripts/lrSv/lrSvVcfToBed.py
@@ -55,30 +55,35 @@
             end = int(info.get("END", pos))
             svLenRaw = int(float(info.get("SVLEN", "0")))
             af = float(info.get("AF", "0"))
             supp = int(info.get("SUPP", "0"))
             ciPos = info.get("CIPOS", "0,0")
             ciEnd = info.get("CIEND", "0,0")
             chr2 = info.get("CHR2", ".")
             strands = info.get("STRANDS", "+-")
             suppVec = info.get("SUPP_VEC", "")
 
             # BED is 0-based half-open
             chromStart = pos - 1
 
             # For INS, END == POS so the item has zero width; expand by 1 bp
             chromEnd = end
+            # For symbolic <DEL>, VCF POS is the padding base before the event
+            # (not deleted); the deleted region is [POS+1, END]. Drop the padding
+            # base from the left so svLen == |SVLEN|. Only DEL moves.
+            if svType == "DEL":
+                chromStart += 1
             if chromEnd <= chromStart:
                 chromEnd = chromStart + 1
 
             # Score: map QUAL to 0-1000
             try:
                 score = min(int(round(float(qual) * 2)), 1000)
             except ValueError:
                 score = 0
 
             # Strand from first character of STRANDS field
             strand = strands[0] if strands and strands[0] in "+-" else "."
 
             color = svColor(svType)
 
             # sampleList from SUPP_VEC