c7e37754a34c3a9406c4546225253d49b2cdf82f
chmalee
  Sat Jun 13 01:00:41 2026 -0700
Stage gnomad v4.1.1 bigBed as release alpha, refs #37351

diff --git src/hg/makeDb/trackDb/human/hg38/gnomad.ra src/hg/makeDb/trackDb/human/hg38/gnomad.ra
index 16237e54e2c..0efe1d1f199 100644
--- src/hg/makeDb/trackDb/human/hg38/gnomad.ra
+++ src/hg/makeDb/trackDb/human/hg38/gnomad.ra
@@ -196,30 +196,31 @@
         detailsTabUrls _dataOffset=/gbdb/hg38/gnomAD/v4.1/genomes/gnomad.v4.1.genomes.details.tab.gz
 
     track gnomadVariantsV4.1.1
     parent gnomadVariants
     compositeTrack on
     shortLabel gnomAD v4.1.1
     longLabel Genome Aggregation Database (gnomAD) Genome and Exome Variants v4.1.1
     type bigBed 9 +
     configureByPopup off
     maxWindowCoverage 200000
     maxItems 50000
     dataVersion Release v4.1.1
     html gnomadV4.1
     priority 0.5
     visibility squish
+    release alpha
 
         track gnomadExomesVariantsV4_1_1
         parent gnomadVariantsV4.1.1 on
         visibility squish
         shortLabel gnomAD v4.1.1 Exomes
         longLabel Genome Aggregation Database (gnomAD) Exomes Variants v4.1.1
         dataVersion Release v4.1.1
         type bigBed 9 +
         itemRgb on
         searchIndex name,_displayName,rsId
         html gnomadV4.1
         bigDataUrl /gbdb/hg38/gnomAD/v4.1.1/exomes/exomes.bb
         priority 2
         labelFields rsId,_displayName
         defaultLabelFields _displayName
@@ -227,30 +228,31 @@
         skipEmptyFields on
         filterValues.annot pLoF,missense,synonymous,other
         filterValuesDefault.annot pLoF,missense,synonymous
         filterValues.FILTER PASS,InbreedingCoeff,RF,AC0,AS_VQSR,indel_stack (chrM only),npg (chrM only)
         filterType.FILTER multipleListAnd
         filterValuesDefault.FILTER PASS
         filterValues.variation_type 3_prime_UTR_variant,5_prime_UTR_variant,NMD_transcript_variant,coding_sequence_variant,frameshift_variant,incomplete_terminal_codon_variant,inframe_deletion,inframe_insertion,intron_variant,mature_miRNA_variant,missense_variant,non_coding_transcript_exon_variant,non_coding_transcript_variant,protein_altering_variant,splice_acceptor_variant,splice_donor_variant,splice_region_variant,start_lost,start_retained_variant,stop_gained,stop_lost,stop_retained_variant,synonymous_variant,transcript_ablation
         filterType.variation_type multipleListOr
         filter.AF 0.0
         filterLabel.AF Minor Allele Frequency Filter
         mouseOver <b>Position</b>: $chrom:${chromStart}-${chromEnd} ($ref/$alt)<br> <b>TotalAF</b>: ${AF} (${AC}/${AN})<br> <b>Genes</b>: $genes<br> <b>Annotation</b>: $annot<br> <b>FILTER</b>: ${FILTER}<br> <b>PopMaxAF</b>: ${grpmax}<br> <b>Homozygous Individuals</b>: ${nhomalt}<br> <b>Hemizygous Individuals (only in chrX & chrY)</b>: ${nhemi}
         url https://gnomad.broadinstitute.org/variant/$s-$<_startPos>-$<ref>-$<alt>?dataset=gnomad_r4
         urlLabel View this variant at gnomAD
         detailsDynamicTable _jsonVep|Variant Effect Predictor,_jsonPopTable|Population Frequencies,_jsonHapTable|Haplotype Frequencies
         detailsTabUrls _dataOffset=/gbdb/hg38/gnomAD/v4.1.1/exomes/gnomad.v4.1.1.exomes.details.tab.gz
+        release alpha
 
         track gnomadGenomesVariantsV4_1_1
         parent gnomadVariantsV4.1.1 on
         visibility squish
         shortLabel gnomAD v4.1.1 Genomes
         longLabel Genome Aggregation Database (gnomAD) Genome Variants v4.1.1
         dataVersion Release v4.1.1
         type bigBed 9 +
         itemRgb on
         searchIndex name,_displayName,rsId
         html gnomadV4.1
         bigDataUrl /gbdb/hg38/gnomAD/v4.1.1/genomes/genomes.bb
         priority 1
         labelFields rsId,_displayName
         defaultLabelFields _displayName
@@ -258,30 +260,31 @@
         skipEmptyFields on
         filterValues.annot pLoF,missense,synonymous,other
         filterValuesDefault.annot pLoF,missense,synonymous
         filterValues.FILTER PASS,InbreedingCoeff,RF,AC0,AS_VQSR,indel_stack (chrM only),npg (chrM only)
         filterType.FILTER multipleListAnd
         filterValuesDefault.FILTER PASS
         filterValues.variation_type 3_prime_UTR_variant,5_prime_UTR_variant,NMD_transcript_variant,coding_sequence_variant,frameshift_variant,incomplete_terminal_codon_variant,inframe_deletion,inframe_insertion,intron_variant,mature_miRNA_variant,missense_variant,non_coding_transcript_exon_variant,non_coding_transcript_variant,protein_altering_variant,splice_acceptor_variant,splice_donor_variant,splice_region_variant,start_lost,start_retained_variant,stop_gained,stop_lost,stop_retained_variant,synonymous_variant,transcript_ablation
         filterType.variation_type multipleListOr
         filter.AF 0.0
         filterLabel.AF Minor Allele Frequency Filter
         mouseOver <b>Position</b>: $chrom:${chromStart}-${chromEnd} ($ref/$alt)<br> <b>TotalAF</b>: ${AF} (${AC}/${AN})<br> <b>Genes</b>: $genes<br> <b>Annotation</b>: $annot<br> <b>FILTER</b>: ${FILTER}<br> <b>PopMaxAF</b>: ${grpmax}<br> <b>Homozygous Individuals</b>: ${nhomalt}<br> <b>Hemizygous Individuals (only in chrX & chrY)</b>: ${nhemi}
         url https://gnomad.broadinstitute.org/variant/$s-$<_startPos>-$<ref>-$<alt>?dataset=gnomad_r4
         urlLabel View this variant at gnomAD
         detailsDynamicTable _jsonVep|Variant Effect Predictor,_jsonPopTable|Population Frequencies,_jsonHapTable|Haplotype Frequencies
         detailsTabUrls _dataOffset=/gbdb/hg38/gnomAD/v4.1.1/genomes/gnomad.v4.1.1.genomes.details.tab.gz
+        release alpha
 
 track gnomadConstraint
 parent gnomadVariants on
 shortLabel gnomAD Mut Constraint
 longLabel Gnocchi: Genome Aggregation Database (gnomAD) non-coding constraint of haploinsufficient variation, includes chrX
 bigDataUrl /gbdb/hg38/gnomAD/mutConstraint/mutConstraint.bw
 type bigWig
 setColorWith /gbdb/hg38/gnomAD/mutConstraint/mutConstraint.color.bb
 windowingFunction minimum
 altColor 0,150,0
 color 150,0,0
 maxHeightPixels 128:40:8
 viewLimitsMax -3:3
 autoScale on
 priority 10