c7b6da0a433f53fdf3c4137a67598d099d9ce1a5
max
  Wed Jan 14 10:52:53 2026 -0800
adding SFARI SPARK to varFreqs supertrack, refs #36642

diff --git src/hg/makeDb/trackDb/human/varFreqs.ra src/hg/makeDb/trackDb/human/varFreqs.ra
index d09171e5d10..39aca767481 100644
--- src/hg/makeDb/trackDb/human/varFreqs.ra
+++ src/hg/makeDb/trackDb/human/varFreqs.ra
@@ -1,263 +1,273 @@
 track varFreqs
 shortLabel Variant Frequencies
 longLabel Variant Frequencies from various cohorts or national projects
 group varRep
 type bed 12
 visibility hide
 superTrack on
 
         track allofus
         shortLabel AllOfUs v7 245k WGS
         longLabel Variant Frequencies: AllOfUs - v7 245k WGS, only with allele count >= 20
         type vcfTabix
         parent varFreqs on
         bigDataUrl /gbdb/$D/varFreqs/allofus/allOfUs.locAncFreq.vcf.gz
         dataVersion V7
         visibility pack
         priority 0.5
 
         track me
         shortLabel Regeneron Million Exomes 983k WES
         longLabel Variant Frequencies: Regeneron One Million Exomes (ME) Project - 983k WGS
         parent varFreqs on
         bigDataUrl /gbdb/$D/varFreqs/mcps/mcps.freq.vcf.gz
         visibility pack
         type vcfTabix
         hapClusterEnabled true
         dataVersion 10/04/2023, v1.1.3
         tableBrowser off
         priority 1
 
         track topmed
         shortLabel NHLBI TOPMED 10 151k WGS
         longLabel Variant Frequencies: NHLBI TOPMED - 151k WGS
         type vcfTabix
         parent varFreqs on
         bigDataUrl /gbdb/$D/varFreqs/topmed/topmed10.vcf.gz
         dataVersion Freeze 10
         visibility pack
         priority 2
 
         track sfariSparkExomes
         shortLabel SFARI Spark 140k WES
         longLabel Variant Frequencies: SFARI SPARK - 140k WES
         type vcfTabix
         parent varFreqs on
-        bigDataUrl /gbdb/$D/varFreqs/sfari/SPARK.iWES_v3.2024_08.deepvariant.sites.vcf.gz
+        bigDataUrl /gbdb/$D/varFreqs/sfari/SPARK.iWES_v3.2024_08.deepvariant.norm.vcf.gz
         dataVersion iWES v3 2024_08
         visibility pack
         priority 2.5
 
+        track sfariSparkWgs
+        shortLabel SFARI Spark 12k WGS
+        longLabel Variant Frequencies: SFARI SPARK - 12,519 WGS
+        type vcfTabix
+        parent varFreqs on
+        bigDataUrl /gbdb/$D/varFreqs/sfari/wgs_12519_genome.deepvariant.norm.vcf.gz
+        dataVersion iWGS v1.1
+        visibility pack
+        priority 2.5
+
         track mcps
         shortLabel Mexico City Prospective Study 10k WGS+141k WES
         longLabel Variant Frequencies: Mexico City Prospective Study (MCPS)
         tableBrowser off
         parent varFreqs on
         bigDataUrl /gbdb/$D/varFreqs/mcps/mcps.freq.vcf.gz
         visibility pack
         type vcfTabix
         dataVersion May 2023 (v1.2.0)
         priority 3
 
         track tommo60kjpn
         shortLabel Japan ToMMO 61k WGS
         longLabel Variant Frequencies: Japan 61k - ToMMO SNV+Indels
         type vcfTabix
         parent varFreqs on
         bigDataUrl /gbdb/$D/varFreqs/tommo61kjpn/tommo-61kjpn-20250616-GRCh38-snvindel-af-autosome.vcf.gz
         visibility pack
         dataVersion 2025-06-16
         priority 5
 
         track ALFA
         compositeTrack on
         parent varFreqs on
         visibility pack
         itemRgb on
         type bigBed 9 + .
         shortLabel NCBI ALFA 408k WGS/WES/array
         longLabel Variant Frequencies: NCBI ALFA (dbGaP data) - 408k mixed WGS/WES/array
         mouseOverField frequency
         html ALFA.html
         filter.score 10
         priority 4
         dataVersion R4
 
              track ALFA_GLB
              parent ALFA on
              shortLabel NCBI ALFA: Global
              bigDataUrl /gbdb/$D/varFreqs/alfa/ALFA_GLB.bb
              type bigBed 9 + .
              url https://www.ncbi.nlm.nih.gov/snp/$$#frequency_tab
              urlLabel NCBI Variation Page
 
              track ALFA_EUR
              parent ALFA on
              shortLabel NCBI ALFA: European
              bigDataUrl /gbdb/$D/varFreqs/alfa/ALFA_EUR.bb
              type bigBed 9 + .
              url https://www.ncbi.nlm.nih.gov/snp/$$#frequency_tab
              urlLabel NCBI Variation Page
 
              track ALFA_AFA
              parent ALFA on
              shortLabel NCBI ALFA: African American
              bigDataUrl /gbdb/$D/varFreqs/alfa/ALFA_AFA.bb
              type bigBed 9 + .
              url https://www.ncbi.nlm.nih.gov/snp/$$#frequency_tab
              urlLabel NCBI Variation Page
 
              track ALFA_AFO
              parent ALFA on
              shortLabel NCBI ALFA: African Others
              bigDataUrl /gbdb/$D/varFreqs/alfa/ALFA_AFO.bb
              type bigBed 9 + .
              url https://www.ncbi.nlm.nih.gov/snp/$$#frequency_tab
              urlLabel NCBI Variation Page
 
              track ALFA_AFR
              parent ALFA on
              shortLabel NCBI ALFA: African
              bigDataUrl /gbdb/$D/varFreqs/alfa/ALFA_AFR.bb
              type bigBed 9 + .
              url https://www.ncbi.nlm.nih.gov/snp/$$#frequency_tab
              urlLabel NCBI Variation Page
 
              track ALFA_EAS
              parent ALFA on
              shortLabel NCBI ALFA: East Asian
              bigDataUrl /gbdb/$D/varFreqs/alfa/ALFA_EAS.bb
              type bigBed 9 + .
              url https://www.ncbi.nlm.nih.gov/snp/$$#frequency_tab
              urlLabel NCBI Variation Page
 
              track ALFA_SAS
              parent ALFA on
              shortLabel NCBI ALFA: South Asian
              bigDataUrl /gbdb/$D/varFreqs/alfa/ALFA_SAS.bb
              type bigBed 9 + .
              url https://www.ncbi.nlm.nih.gov/snp/$$#frequency_tab
              urlLabel NCBI Variation Page
 
              track ALFA_OAS
              parent ALFA on
              shortLabel NCBI ALFA: Other Asian
              bigDataUrl /gbdb/$D/varFreqs/alfa/ALFA_OAS.bb
              type bigBed 9 + .
              url https://www.ncbi.nlm.nih.gov/snp/$$#frequency_tab
              urlLabel NCBI Variation Page
 
              track ALFA_ASN
              parent ALFA on
              shortLabel NCBI ALFA: Asian
              bigDataUrl /gbdb/$D/varFreqs/alfa/ALFA_ASN.bb
              type bigBed 9 + .
              url https://www.ncbi.nlm.nih.gov/snp/$$#frequency_tab
              urlLabel NCBI Variation Page
 
              track ALFA_LAC
              parent ALFA on
              shortLabel NCBI ALFA: Latin American 1
              bigDataUrl /gbdb/$D/varFreqs/alfa/ALFA_LAC.bb
              type bigBed 9 + .
              url https://www.ncbi.nlm.nih.gov/snp/$$#frequency_tab
              urlLabel NCBI Variation Page
 
              track ALFA_LEN
              parent ALFA on
              shortLabel NCBI ALFA: Latin American 2
              bigDataUrl /gbdb/$D/varFreqs/alfa/ALFA_LEN.bb
              type bigBed 9 + .
              url https://www.ncbi.nlm.nih.gov/snp/$$#frequency_tab
              urlLabel NCBI Variation Page
 
              track ALFA_OTR
              parent ALFA on
              shortLabel NCBI ALFA: Other
              bigDataUrl /gbdb/$D/varFreqs/alfa/ALFA_OTR.bb
              type bigBed 9 + .
              url https://www.ncbi.nlm.nih.gov/snp/$$#frequency_tab
              urlLabel NCBI Variation Page
 
         track finngen
         parent varFreqs on
         visibility pack
         type vcfTabix
         shortLabel Finnland Finngen 500k imputed
         longLabel Variant Frequencies: Finnland Finngen - 500k samples, arrays, imputation used 8.5k WGS
         priority 4.5
         bigDataUrl /gbdb/$D/varFreqs/finngen/finnge_R12_annotated_variants_v1.vcf.gz
         dataVersion R12
         tableBrowser off
 
         track swefreq
         parent varFreqs on
         visibility pack
         type vcfTabix
         shortLabel Sweden SweGen 1k WGS
         longLabel Variant Frequencies: Sweden SweGen - 1k WGS
         priority 4.7
         bigDataUrl /gbdb/$D/varFreqs/swefreq/swegen_frequencies_fixploidy_GRCh38_20190204.vcf.gz
         dataVersion 20251201
         tableBrowser off
 
         track gasp
         shortLabel GenomeAsia Pilot Subs 1.7k WGS
         longLabel Variant Frequencies: GenomeAsia Pilot - Substitutions
         type vcfTabix
         parent varFreqs on
         bigDataUrl /gbdb/$D/varFreqs/ga100k/ga100k.subst.vcf.gz
         visibility pack
 
         track gaspIndel
         shortLabel GenomeAsia Pilot Indels 1.7k WGS
         longLabel Variant Frequencies: GenomeAsia Pilot - Indels
         type vcfTabix
         parent varFreqs on
         bigDataUrl /gbdb/$D/varFreqs/ga100k/All.indels.annot.cont_withmaf.vcf.gz
         visibility pack
 
         track abraom
         shortLabel Brazil ABraOM 1k WGS
         longLabel Variant Frequencies: ABraOM Brazil - 1,171 unrelated individuals
         type vcfTabix
         parent varFreqs on
         bigDataUrl /gbdb/$D/varFreqs/abraom/abraom.vcf.gz
         visibility pack
         dataVersion SABE-WGS-1171 Sep 2020
 
         track indigenomes
         shortLabel India IndiGenomes 1k WGS
         longLabel Variant Frequencies: IndiGenomes India - 1,029 samples
         type vcfTabix
         parent varFreqs on
         bigDataUrl /gbdb/$D/varFreqs/indigenomes/IndiGenomes_Variants.vcf.gz
         visibility pack
 
         track kova
         shortLabel Korea KOVA 1.9k WGS+3.5k WES
         longLabel Variant Frequencies: KOVA Korea - 5305 samples, 1.9k WGS+3.5k WES
         type vcfTabix
         parent varFreqs on
         bigDataUrl /gbdb/$D/varFreqs/kova/kova.v7.vcf.gz
         visibility pack
         tableBrowser off
         dataVersion V7
 
         track npm
         shortLabel Singapore NPM 9.7k WGS
         longLabel Variant Frequencies: NPM Singapore - 9,770 WGS samples
         type vcfTabix
         parent varFreqs on
         bigDataUrl /gbdb/$D/varFreqs/npm/SG10K_Health_r5.3.2.sites.vcf.bgz
         visibility pack
         tableBrowser off
         dataVersion r5.3.2
 
         track saudi
         shortLabel Saudi Genome Project 302 WGS
         longLabel Variant Frequencies: Saudi Genome Project - 302 WGS samples
         type vcfTabix
         parent varFreqs on
         bigDataUrl /gbdb/$D/varFreqs/saudi/saudi.vcf.gz
         visibility pack