28bfc5e8e4301c0955eac938490458282438cf49
max
  Tue Nov 4 07:28:44 2025 -0800
adding HGDP and alfa docs page to var freqs track

diff --git src/hg/makeDb/trackDb/human/varFreqs.ra src/hg/makeDb/trackDb/human/varFreqs.ra
index 56811e86168..82ab553b45d 100644
--- src/hg/makeDb/trackDb/human/varFreqs.ra
+++ src/hg/makeDb/trackDb/human/varFreqs.ra
@@ -1,168 +1,202 @@
 track varFreqs
 shortLabel Variant Frequencies
 longLabel Variant Frequencies from various population- or cohort-specific Projects
 group varRep
 type bed 12
 visibility hide
 superTrack on
 
         track mexbb
         shortLabel Mexico Biobank
         longLabel Variant Frequencies: Mexico Biobank
         tableBrowser off
         parent varFreqs on
         bigDataUrl /gbdb/$D/varFreqs/mexbb/MXBv2.vcf.gz
         visibility pack
         type vcfTabix
         hapClusterEnabled true
         dataVersion Nov 2025
+        priority 0.5
 
         track mcps
         shortLabel Mexico City Prospective Study 
         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 me
         shortLabel Regeneron Million Exomes
         longLabel Variant Frequencies: Regeneron One Million Exomes (ME) Project
         tableBrowser off
         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
+        priority 1
 
         track topmed
         shortLabel NHLBI TOPMED 10
         longLabel Variant Frequencies: NHLBI TOPMED
         type vcfTabix
         parent varFreqs on
         bigDataUrl /gbdb/$D/varFreqs/topmed/topmed10.vcf.gz
         dataVersion Freeze 10
         visibility pack
+        priority 2
 
-        track gasp
-        shortLabel GenomeAsia Pilot Subs
-        longLabel Variant Frequencies: GenomeAsia Pilot Substitutions
+        track tommo60kjpn
+        shortLabel Japan 61k ToMMO 
+        longLabel Variant Frequencies: Japan 61k - ToMMO SNV+Indels
         type vcfTabix
         parent varFreqs on
-        bigDataUrl /gbdb/$D/varFreqs/ga100k/ga100k.subst.vcf.gz
+        bigDataUrl /gbdb/$D/varFreqs/tommo61kjpn/tommo-61kjpn-20250616-GRCh38-snvindel-af-autosome.vcf.gz
         visibility pack
-        #dataVersion GAsP Pilot: 1,739 individuals
+        dataVersion 2025-06-16
+        priority 5
 
         track ALFA
         compositeTrack on
-        parent varFreqs
+        parent varFreqs on
         visibility pack
         itemRgb on
         type bigBed 9 + .
         shortLabel NCBI ALFA 
-        longLabel NCBI ALFA: Allele Frequency Aggregator from dbGap submissions
+        longLabel Variant Frequencies: NCBI ALFA (Allele Frequency Aggregator) from dbGaP
         mouseOverField frequency
         html ALFA.html
         filter.score 10
         #filterByRange.score on
         #filterLimits.score 400:500
         #filterValues.name rs1424773263,rs2531320
+        priority 4
 
              track ALFA_GLB
              parent ALFA on
              shortLabel NCBI ALFA: Global
-             bigDataUrl /gbdb/hg38/varFreqs/alfa/ALFA_GLB.bb
+             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/hg38/varFreqs/alfa/ALFA_EUR.bb
+             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/hg38/varFreqs/alfa/ALFA_AFA.bb
+             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/hg38/varFreqs/alfa/ALFA_AFO.bb
+             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/hg38/varFreqs/alfa/ALFA_AFR.bb
+             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/hg38/varFreqs/alfa/ALFA_EAS.bb
+             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/hg38/varFreqs/alfa/ALFA_SAS.bb
+             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/hg38/varFreqs/alfa/ALFA_OAS.bb
+             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/hg38/varFreqs/alfa/ALFA_ASN.bb
+             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/hg38/varFreqs/alfa/ALFA_LAC.bb
+             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/hg38/varFreqs/alfa/ALFA_LEN.bb
+             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/hg38/varFreqs/alfa/ALFA_OTR.bb
+             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 hgdp
+        shortLabel Human Genome Diversity Project
+        longLabel Variant Frequencies: Human Genome Diversity Project (HGDP) - 1043 samples from indigenous and isolated populations
+        type vcfTabix
+        parent varFreqs on
+        bigDataUrl /gbdb/$D/varFreqs/hgdp/hgdp_wgs.20190516.full.vcf.gz
+        visibility pack
+        dataVersion 2019-05-16
+
+        track gasp
+        shortLabel GenomeAsia Pilot Subs
+        longLabel Variant Frequencies: GenomeAsia Pilot - Substitutions
+        type vcfTabix
+        parent varFreqs on
+        bigDataUrl /gbdb/$D/varFreqs/ga100k/ga100k.subst.vcf.gz
+        visibility pack
+        #dataVersion GAsP Pilot: 1,739 individuals
+
+        track gaspIndel
+        shortLabel GenomeAsia Pilot Indels
+        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
+        #dataVersion GAsP Pilot: 1,739 individuals
+