0656b0a9ad98986ef3944b6ceaf305ab08ca4e39
max
  Fri Jul 24 01:10:13 2026 -0700
noyvertSv: swap UK Biobank r2 filter for leave-one-out metrics, revise description

Per author (Boris Noyvert) request, replace the r2Ukb (UK Biobank imputation
r2) filter with r2Loo and concordanceLoo, the primary SV imputation quality
measures for the multi-ancestry reference panel (r2Ukb mainly reflects
European-ancestry performance). Both fields already exist in noyvert.bb, so
this is a trackDb-only change. Also update the description page with the
author's revised text, including a comparison with the 1KG ONT Vienna dataset. refs #37888

diff --git src/hg/makeDb/doc/hg38/lrSv.txt src/hg/makeDb/doc/hg38/lrSv.txt
index 07a7fe15cc3..df579e947d4 100644
--- src/hg/makeDb/doc/hg38/lrSv.txt
+++ src/hg/makeDb/doc/hg38/lrSv.txt
@@ -757,15 +757,28 @@
 bigBedToBed NIH_CARD_longReadSVs.bb stdout \
   | python3 $HOME/kent/src/hg/makeDb/scripts/lrSv/lrSvCardBbToBed.py /dev/stdin cardSv.bed
 # CARD: 228,855 input records written; by type: DEL=101,570, DUP=1,
 #       INS=126,853, INV=431
 bedSort cardSv.bed cardSv.sorted.bed
 bedToBigBed -type=bed9+ -as=$HOME/kent/src/hg/makeDb/scripts/lrSv/lrSvCard.as \
     -tab cardSv.sorted.bed /hive/data/genomes/hg38/chrom.sizes cardSv.bb
 # Max allele counts: AC=702 (2x351), nabecAc=410 (2x205), hbccAc=292 (2x146).
 # trackDb filter ranges/labels updated to allele counts; mouseOver and the
 # cardSv.html / lrSv.html wording changed from "carriers" to "allele counts".
 #
 # Re-ran the merge so lrSvAll carries CARD's allele counts (databases.tsv
 # unchanged; CARD still contributes via valueField=AC):
 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).