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/lrSvAprVcfToBed.py src/hg/makeDb/scripts/lrSv/lrSvAprVcfToBed.py
index 11742f0293c..34cdc5e9ac0 100755
--- src/hg/makeDb/scripts/lrSv/lrSvAprVcfToBed.py
+++ src/hg/makeDb/scripts/lrSv/lrSvAprVcfToBed.py
@@ -130,30 +130,35 @@
                 if i < len(ac_list):
                     ac_sum += _int(ac_list[i])
                 num_pass += 1
 
             if num_pass == 0:
                 skipped_no_sv_alt += 1
                 continue
 
             sv_type = next(iter(types)) if len(types) == 1 else "MIXED"
             sv_type = normalizeSvType(sv_type)
             rgb = svColor(sv_type)
 
             pos0 = int(pos) - 1
             start = pos0
             end = start + max(ref_len, 1)
+            # For DEL, POS is the non-deleted anchor base; drop it from the left
+            # (end already = pos-1+ref_len). The shared prefix is >=1 base so this
+            # never over-shifts. Only DEL moves; INS/MIXED keep the anchor.
+            if sv_type == "DEL":
+                start += 1
             af = (ac_sum / an) if an else 0.0
             score = min(1000, max(0, int(round(af * 1000))))
 
             svLen = end - start
             if sv_type == "INS":
                 insLen = max_ins
             else:
                 insLen = 0
 
             featLen = insLen if sv_type in ("INS", "MEI") else svLen
             name = svName(sv_type, featLen, ac_sum)
 
             row = [
                 chrom, str(start), str(end),
                 name,