d92e36dbbee172d6bb81a751eb8bb935f356890c
max
  Fri Jul 17 09:31:28 2026 -0700
lrSv: add cardSv and noyvertSv to the lrSvAll merged track

#Preview2 week - bugs introduced now will need a build patch to fix
Append NIH CARD 351 (AC/alleleFreq) and Noyvert 888 (AC/AF) to databases.tsv
and re-run lrSvMergeAll.py: 16 source databases now, 3,018,404 input variants
merged to 2,582,278 (was 14 dbs, 2,317,508). Regenerated lrSvAll.ra
(filterValues.sources + sourceCount 1:16) and updated the container summary
table. refs #36258

diff --git src/hg/makeDb/doc/hg38/lrSv.txt src/hg/makeDb/doc/hg38/lrSv.txt
index c0695510eaf..4853d64177a 100644
--- src/hg/makeDb/doc/hg38/lrSv.txt
+++ src/hg/makeDb/doc/hg38/lrSv.txt
@@ -714,15 +714,26 @@
 #    shared lrSv convention (see lrSvCommon.py): 1 bp for INS/BND, the interval
 #    length for DEL/INV/DUP. The inserted-sequence length lives in insLen (INS
 #    only; the source SVLEN). This is why the summary table on the lrSv.html
 #    container page shows min=median=1 for this dataset (INS dominate).
 #  - AC/AN are approximate (the source has only AF): AN = round(2*888*(1-missing
 #    rate)); AC = round(AF*AN). Documented as approximate in trackDb and on the
 #    track description page.
 #  - BND mate breakend loci are stored in the secondBp field with the Sniffles2
 #    'CHR' prefix lower-cased to 'chr' (some mates land on alt/random/Un/M/EBV
 #    contigs; the primary breakpoint is always on a standard autosome).
 #  - UKB_SVWAS_signif is reformatted comma-free into ukbGwas, with the number of
 #    significant trait associations in nGwas (for filtering).
 #  - Colors from the shared svColor() palette in lrSvCommon.py.
 #
 # Not added to the lrSvAll merge for now.
+
+# Added cardSv (NIH CARD 351) and noyvertSv (Noyvert 888) to the lrSvAll merge:
+# both appended to databases.tsv (CARD uses alleleFreq for max-AF aggregation,
+# Noyvert888 uses AF) and the merge re-run. The merge auto-regenerates
+# lrSvAll.as and trackDb/human/lrSvAll.ra (now 16 source databases,
+# filter.sourceCount 1:16).
+python3 ~/kent/src/hg/makeDb/scripts/lrSv/lrSvMergeAll.py
+# 3,018,404 input variants -> 2,582,278 merged (14.4% dedup), 16 databases
+# (was 2,682,104 -> 2,317,508 with 14 databases). All INS store svLen=1 across
+# every subtrack, so insertions merge on insLen; the merged median svLen is 1
+# (INS are 1.65M of 2.58M rows).