7bdcd030cdf434c72f3f6a492ee8f84372c752c7
max
  Sat Jul 25 19:22:57 2026 -0700
noyvertSv: note the Boehringer/Vienna relationship and call-level overlap

The Noyvert panel is an independent reprocessing of the same ONT reads as the
1KG ONT Vienna track (Schloissnig et al. 2025). Add a description sentence with
the deletion counts (~38k vs ~58k, ~12k shared at 50% reciprocal overlap) and
the concordance both ways (about a third of this track's deletions and a fifth
of Vienna's at 50%, a quarter and a sixth at 90%; ~a quarter of insertions
match within 100 bp). Overlap analysis recorded in the makeDoc. refs #37888

diff --git src/hg/makeDb/doc/hg38/lrSv.txt src/hg/makeDb/doc/hg38/lrSv.txt
index baf41227165..039a46ecbcf 100644
--- src/hg/makeDb/doc/hg38/lrSv.txt
+++ src/hg/makeDb/doc/hg38/lrSv.txt
@@ -770,15 +770,28 @@
 python3 ~/kent/src/hg/makeDb/scripts/lrSv/lrSvMergeAll.py
 # 3,018,404 input -> 2,582,278 merged, 16 databases (unchanged structure).
 
 ##########
 # 2026-07-24 Claude max
 #
 # noyvertSv: per author (Boris Noyvert) request, replaced the UK Biobank
 # imputation-r2 filter (r2Ukb) with two leave-one-out reference-panel quality
 # filters, r2Loo and concordanceLoo, which are the primary SV imputation
 # quality measures for the multi-ancestry panel (r2Ukb mainly reflects
 # European-ancestry performance). trackDb-only change; both fields already
 # exist in noyvert.bb (floats, 0:1), so no rebuild was needed. Also replaced
 # the Description text on noyvertSv.html with the author's revised version
 # (reordered, plus a comparison with the 1KG ONT Vienna dataset, Schloissnig
 # et al. 2025).
+
+# Added a clarifying sentence to noyvertSv.html: the Noyvert (Boehringer) panel
+# is an independent reprocessing of the same ONT reads as the 1KG ONT Vienna
+# track (Schloissnig et al. 2025), plus a rough call-level overlap on hg38.
+# Overlap analysis (scratch, overlapSelect + bedtools, Boehringer vs Vienna):
+#   DEL (Boehringer 38,459 / Vienna 58,637): reciprocal >=50% = 12,529 (33%);
+#       >=90% = 9,136 (24%); >=10% = 15,127 (39%). Cross-checked with
+#       bedtools intersect -f .5 -r (11,802). Reverse direction ~ same.
+#   INS (Boehringer 59,953 / Vienna 73,298): within +-100bp and insLen ratio
+#       >=0.5 = 13,535 (23%); plateaus at ~26% out to +-1000bp (so not a
+#       liftOver positional-shift artifact - Vienna hg38 is lifted from CHM13).
+#   INV/DUP/BND have no comparable Vienna type (Vienna calls only DEL/INS/CPX).
+# Only trackDb HTML changed; no data rebuild.