9cedfa38c14068c79dec89f76c606ee22b3f931a
max
  Wed Sep 30 15:02:37 2026 -0700
phasedVars: new subtrack hgdp1kSnv, a 17GB version of the 3.5TB gnomAD HGDP+1000G genotype VCF with only SNVs with AC>5 and only GT, so haplotype clustering can be shown up to 5Mbp, refs #37306

diff --git src/hg/makeDb/trackDb/human/phasedVars.ra src/hg/makeDb/trackDb/human/phasedVars.ra
index 8ee60ac4909..9da95cd6d6b 100644
--- src/hg/makeDb/trackDb/human/phasedVars.ra
+++ src/hg/makeDb/trackDb/human/phasedVars.ra
@@ -1,76 +1,90 @@
 track phasedVars
 shortLabel Phased Variants
 longLabel Phased Variants from various sequencing projects
 group varRep
 type bed 12
 visibility hide
 superTrack on
 
         track mexbb
         shortLabel Mexico Biobank, 6k Array
         longLabel Phased Variants: Mexico Biobank 6k Array
         tableBrowser off
         parent phasedVars on
         bigDataUrl /gbdb/$D/phasedVars/mexbb/MXBv2.vcf.gz
         visibility pack
         type vcfTabix
         hapClusterEnabled true
         dataVersion Nov 2025 (hg38 lift)
         priority 1
         html phasedVars.html
 
         track hgdp
         shortLabel Human Genome Diversity Project, 1k WGS
         longLabel Phased Variants: Human Genome Diversity Project (HGDP) - 1043 samples, isolated populations
         type vcfTabix
         parent phasedVars on
         bigDataUrl /gbdb/$D/phasedVars/hgdp/hgdp_wgs.20190516.full.vcf.gz
         visibility pack
         dataVersion 2019-05-16
         priority 2
         html phasedVars.html
 
         track sgdp
         shortLabel Simons Genome Diversity Project 0.3k WGS
         longLabel Phased Variants: Simons Genome Diversity Project - 279 samples, unmixed populations
         type vcfTabix
         parent phasedVars on
         bigDataUrl /gbdb/$D/phasedVars/sgdp/SGDP.nh2.vcf.gz
         visibility pack
         dataVersion 2016-12-07 public (hg38 lift)
         priority 4
         html phasedVars.html
 
         track hgdp1k
         shortLabel gnomAD HGDP+1000G 4k WGS
         longLabel Phased Variants: gnomAD HGDP + 1000 genomes callset - 4094 whole genomes, 80 populations
         type vcfTabix
         parent phasedVars on
         bigDataUrl /gbdb/$D/phasedVars/hgdp1k/gnomad.genomes.v3.1.2.hgdp_tgp.vcf.gz
         visibility pack
         dataVersion v 3.1.2
         priority 5
         html phasedVars.html
 
+        track hgdp1kSnv
+        shortLabel gnomAD HGDP+1000G SNVs AC>5
+        longLabel Phased Variants: gnomAD HGDP + 1000 genomes callset - SNVs with allele count > 5 only, faster display
+        type vcfTabix
+        parent phasedVars
+        bigDataUrl /gbdb/$D/phasedVars/hgdp1k/hgdp1k.snvAc6.vcf.gz
+        maxWindowToDraw 5000000
+        maxItems 200000
+        visibility pack
+        dataVersion v 3.1.2
+        release alpha
+        priority 6
+        html phasedVars.html
+
         track han945SvVcf
         parent phasedVars
         bigDataUrl /gbdb/$D/phasedVars/han945genotypes.vcf.gz
         shortLabel SVs from 945 Han Chinese
         longLabel Phased Variants: Structural variants from 945 Han Chinese SVs
         type vcfTabix
         visibility dense
         release alpha
         priority 10
 
         track lrSv1kgOntPhased
         parent phasedVars
         bigDataUrl /gbdb/$D/phasedVars/1kgOntPhased.vcf.gz
         shortLabel SVs from 1000G ONT
         longLabel Phased Variants: Structural variants from 1,019 diverse humans (1000 Genomes Vienna ONT, shapeit5)
         type vcfTabix
         visibility dense
         sampleColorFile Superpopulation=/gbdb/$D/phasedVars/1kgOntPhased.superpopColors.txt
         sampleMetadataFile /gbdb/$D/phasedVars/1kgOntPhased.sampleMeta.txt
         release alpha
         priority 11