dc1e0e76dbe49861bd0ebe8db64e27f587737794
max
  Mon Mar 30 15:40:03 2026 -0700
adding two more phased variants tracks, refs #37306

diff --git src/hg/makeDb/doc/hg38/varFreqs.txt src/hg/makeDb/doc/hg38/varFreqs.txt
index e7f35b77bcc..7de0e6a41e4 100644
--- src/hg/makeDb/doc/hg38/varFreqs.txt
+++ src/hg/makeDb/doc/hg38/varFreqs.txt
@@ -203,15 +203,25 @@
 # finnge_R12_annotated_variants_v1.gz (32 GB TSV)                                                                          
 # Convert TSV to VCF using custom Python script (written by Claude Opus 4.5)                                               
 python ~/kent/src/hg/makeDb/scripts/varFreqs/finngen_to_vcf.py \                                                                    
     finnge_R12_annotated_variants_v1.gz \                                                                                    
     finnge_R12_annotated_variants_v1.vcf                                                                                     
 # Compress and index                                                                                                       
 bgzip finnge_R12_annotated_variants_v1.vcf -@8                                                                             
 tabix -p vcf finnge_R12_annotated_variants_v1.vcf.gz                                                                       
 
 # All of Us, Max Feb 2026
 # Received from Qudsi at UCSC in the Ioannidis group via phoenix
 # only concated and ran tabix on it
 cd /hive/data/genomes/hg38/bed/varFreqs/allofus/
 bcftools concat --threads 16 -Oz -o allOfUs.locAncFreq.vcf.gz clean/allele_freq_chr{1..22}.NW.clean.conf90.oneline.vcf.gz
 tabix allOfUs.locAncFreq.vcf.gz
+
+##########
+# 2026-03-27 Claude max
+
+# Two phased SV VCF tracks moved into phasedVars superTrack from lrSv:
+# - han945SvVcf: Per-sample genotypes for 945 Han Chinese SVs
+# - lrSv1kgOntPhased: Phased SVs from 1,019 diverse humans (1KG ONT)
+# Data files remain in /hive/data/genomes/hg38/bed/lrSv/
+# Symlinks moved from /gbdb/{hg38,hs1}/lrSv/ to /gbdb/{hg38,hs1}/phasedVars/
+# Build documentation for these tracks is in lrSv.txt