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/lrSvGa4kSvVcfToBed.py src/hg/makeDb/scripts/lrSv/lrSvGa4kSvVcfToBed.py
index f20f95fe925..8464fe8a202 100644
--- src/hg/makeDb/scripts/lrSv/lrSvGa4kSvVcfToBed.py
+++ src/hg/makeDb/scripts/lrSv/lrSvGa4kSvVcfToBed.py
@@ -48,30 +48,35 @@
             chrom = fields[0]
             pos = int(fields[1])
             rowName = fields[2]
             info = parseInfo(fields[7])
 
             svTypeRaw = info.get("SVTYPE", ".")
             svType = normalizeSvType(svTypeRaw)
             end = int(info.get("END", pos))
             svLenRaw = int(float(info.get("SVLEN", "0")))
             af = float(info.get("SVF", "0"))
             svc = int(info.get("SVC", "0"))
             svn = int(info.get("SVN", "0"))
 
             chromStart = pos - 1
             chromEnd = end
+            # POS is the non-deleted anchor base; drop it from the left of DEL
+            # intervals so svLen == |SVLEN| and coordinates match anchor-excluded
+            # callsets. INS/other keep the anchor-based position.
+            if svType == "DEL":
+                chromStart += 1
             if chromEnd <= chromStart:
                 chromEnd = chromStart + 1
 
             svLen = chromEnd - chromStart
             if svType in ("INS", "MEI"):
                 insLen = abs(svLenRaw)
             else:
                 insLen = 0
 
             # AC: GA4K site-level VCF has no AC. Approximate as 2 * svn * af
             # (diploid alleles * variant frequency).
             ac = int(round(2 * svn * af))
 
             color = SV_COLORS.get(svType, "100,100,100")