526213b2893134217a300ff913e11b4e98d67991
max
  Mon Apr 20 08:50:10 2026 -0700
lrSv: add cpc1Sv and aprSv pangenome SV subtracks (hg38, hs1)

cpc1Sv: 97,205 SVs from the CPC + HPRC Phase 1 pangenome (Gao et al 2023,
Nature; PMID 37316654) built on T2T-CHM13v2, with 53 Chinese and 47 HPRC
samples. Each graph snarl site is shown as one item with alt alleles
classified by length delta (INS/DEL/CPX, 50 bp threshold) and collapsed.

aprSv: 103,077 SVs from the Arabic Pangenome Reference (Nassir et al.
2025, Nat Commun; PMID 40707445) built on T2T-CHM13v2 from 53 UAE-resident
Arab individuals. Same multi-allele classification as cpc1Sv, with alt
alleles iterated within each multi-allelic row.

Both tracks load natively on hs1 and are lifted to hg38 with
hs1ToHg38.over.chain.gz.

refs #36258

diff --git src/hg/makeDb/scripts/lrSv/lrSvCpc1Build.sh src/hg/makeDb/scripts/lrSv/lrSvCpc1Build.sh
new file mode 100755
index 00000000000..a12e65a1b82
--- /dev/null
+++ src/hg/makeDb/scripts/lrSv/lrSvCpc1Build.sh
@@ -0,0 +1,41 @@
+#!/usr/bin/env bash
+# Build cpc1 lrSv subtrack for hs1 (native) and hg38 (lifted).
+# Run from /hive/data/genomes/hg38/bed/lrSv/cpc1/
+
+set -euo pipefail
+
+SCRIPTS=/cluster/home/max/kent/src/hg/makeDb/scripts/lrSv
+AS="$SCRIPTS/lrSvCpc1.as"
+VCF=CPC.HPRC.Phase1.processed.SVs.normed.vcf.gz
+HS1_SIZES=/hive/data/genomes/hs1/chrom.sizes
+HG38_SIZES=/hive/data/genomes/hg38/chrom.sizes
+CHAIN=/gbdb/hs1/liftOver/hs1ToHg38.over.chain.gz
+
+# --- Build hs1 native bed ---
+echo "[$(date +%T)] converting VCF to hs1 bed..."
+zcat "$VCF" | python3 "$SCRIPTS/lrSvCpc1VcfToBed.py" /dev/stdin cpc1.hs1.bed "$HS1_SIZES"
+
+echo "[$(date +%T)] sorting hs1 bed..."
+bedSort cpc1.hs1.bed cpc1.hs1.sorted.bed
+
+echo "[$(date +%T)] building hs1 bigBed..."
+bedToBigBed -type=bed9+ -tab -as="$AS" \
+    cpc1.hs1.sorted.bed "$HS1_SIZES" cpc1.hs1.bb
+
+# --- liftOver to hg38 ---
+echo "[$(date +%T)] lifting to hg38..."
+liftOver -tab -bedPlus=9 cpc1.hs1.bed "$CHAIN" \
+    cpc1.hg38.bed cpc1.hs1.unmapped.bed
+
+echo "  hg38 mapped:   $(wc -l < cpc1.hg38.bed)"
+echo "  hg38 unmapped: $(grep -cv '^#' cpc1.hs1.unmapped.bed || true)"
+
+echo "[$(date +%T)] sorting hg38 bed..."
+bedSort cpc1.hg38.bed cpc1.hg38.sorted.bed
+
+echo "[$(date +%T)] building hg38 bigBed..."
+bedToBigBed -type=bed9+ -tab -as="$AS" \
+    cpc1.hg38.sorted.bed "$HG38_SIZES" cpc1.hg38.bb
+
+ls -lh cpc1.hs1.bb cpc1.hg38.bb
+echo "[$(date +%T)] done."