hub IGV
shortLabel UCSC Hosted Annotations
longLabel IGV hosted annotations.
useOneFile on

genome hg38
groups groups.txt

track refseqSelect
type refgene
shortLabel Refseq Select
longLabel Refseq Select
group genes
bigDataUrl https://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/ncbiRefSeqSelect.txt.gz
html https://www.ncbi.nlm.nih.gov/refseq/refseq_select/

track refseqCurated
type refgene
shortLabel Refseq Curated
longLabel Refseq Curated
group genes
bigDataUrl https://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/ncbiRefSeqCurated.txt.gz
html https://www.ncbi.nlm.nih.gov/refseq/refseq_select/

track refseqAll
type refgene
shortLabel Refseq All
longLabel Refseq All
group genes
bigDataUrl https://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/ncbiRefSeq.txt.gz
html https://www.ncbi.nlm.nih.gov/refseq/refseq_select/

track maneRefseq
type bigBed
shortLabel MANE v1.0 - Refseq
longLabel MANE v1.0 transcripts with RefSeq labels
group genes
bigDataUrl https://ftp.ncbi.nlm.nih.gov/refseq/MANE/trackhub/data/release_1.0/MANE.GRCh38.v1.0.refseq.bb
labelFields nucAcc
html https://www.ncbi.nlm.nih.gov/refseq/MANE/

track maneRefseq
type bigBed
shortLabel MANE v1.0 - Ensembl
longLabel MANE v1.0 transcripts with Ensembl labels
group genes
bigDataUrl https://ftp.ncbi.nlm.nih.gov/refseq/MANE/trackhub/data/release_1.0/MANE.GRCh38.v1.0.ensembl.bb
labelFields nucAcc
html https://www.ncbi.nlm.nih.gov/refseq/MANE/

track gencode44
type bigBed
shortLabel Gencode v44
longLabel Gencode v44
group genes
bigDataUrl https://hgdownload.soe.ucsc.edu/gbdb/hg38/gencode/gencodeV44.bb
labelFields transcript_name
html https://www.gencodegenes.org

track gencode47
type bigBed
shortLabel Gencode v47
longLabel Gencode v47
group genes
bigDataUrl https://hgdownload.soe.ucsc.edu/gbdb/hg38/gencode/gencodeV47.bb
labelFields geneName
html https://www.gencodegenes.org

track clinvar
type bigBed
shortLabel ClinVar
longLabel ClinVar Variants
group phenDis
bigDataUrl http://hgdownload.soe.ucsc.edu/gbdb/hg19/bbi/clinvar/clinvarMain.bb
html https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=clinvar

track civic
type bigBed
shortLabel CIViC
longLabel CIViC - Expert & crowd-sourced cancer variant interpretation
group phenDis
bigDataUrl https://hgdownload.soe.ucsc.edu/gbdb/hg38/civic/civic.bb
html https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=civic

#track cosmic
#type bigBed
#shortLabel COSMIC
#longLabel Catalogue of Somatic Mutations in Cancer
#group phenDis
#bigDataUrl https://hgdownload.soe.ucsc.edu/gbdb/hg38/cosmic/cosmic.bb
#html https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=cosmicMuts

track clinGenHaplo
type bigBed
shortLabel ClinGen Haploinsufficiency
longLabel ClinGen Dosage Sensitivity Map - Haploinsufficiency
group phenDis
bigDataUrl https://hgdownload.soe.ucsc.edu/gbdb/hg38/bbi/clinGen/clinGenHaplo.bb
html https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=clinGenComp

track clinGenTriplo
type bigBed
shortLabel ClinGen Triplosensitivity
longLabel ClinGen Dosage Sensitivity Map - Triplosensitivity
group phenDis
bigDataUrl https://hgdownload.soe.ucsc.edu/gbdb/hg38/bbi/clinGen/clinGenTriplo.bb
html https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=clinGenComp

track clinGenGeneDisease
type bigBed
shortLabel ClinGen Validity
longLabel ClinGen Gene-Disease Validity Classification
group phenDis
bigDataUrl https://hgdownload.soe.ucsc.edu/gbdb/hg38/bbi/clinGen/clinGenGeneDisease.bb
html https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=clinGenComp

track clinGenCspec
type bigBed
shortLabel ClinGen VCEP Spec
longLabel Clingen CSpec Variant Interpretation VCEP Specifications
group phenDis
bigDataUrl https://hgdownload.soe.ucsc.edu/gbdb/hg38/bbi/clinGen/clinGenCspec.bb
html https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=clinGenComp

track genCC
type bigBed
shortLabel GenCC
longLabel  	GenCC: The Gene Curation Coalition Annotations
group phenDis
bigDataUrl http://hgdownload.soe.ucsc.edu/gbdb/hg38/bbi/genCC.bb
html https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=genCC

track dbSNP155
type bigBed
shortLabel dbSNP 155
longLabel dbSNP 155
group var
bigDataUrl https://hgdownload.soe.ucsc.edu/gbdb/hg38/snp/dbSnp155.bb
html https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=dbSnp155Composite

track giabAsh
type vcfTabix
shortLabel GIAB Ashkenazi Trio
longLabel Genome In a Bottle Ashkenazi Trio
group var
bigDataUrl https://hgdownload.soe.ucsc.edu/gbdb/hg38/giab/AshkenazimTrio/merged.vcf.gz
bigDataIndex https://hgdownload.soe.ucsc.edu/gbdb/hg38/giab/AshkenazimTrio/merged.vcf.gz.tbi
html https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=giab

track giabChinese
type vcfTabix
shortLabel GIAB Chinese Trio
longLabel Genome In a Bottle Chinese Trio
group var
bigDataUrl https://hgdownload.soe.ucsc.edu/gbdb/hg38/giab/ChineseTrio/merged.vcf.gz
bigDataIndex https://hgdownload.soe.ucsc.edu/gbdb/hg38/giab/ChineseTrio/merged.vcf.gz.tbi
html https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=giab

track giabAsh
type bigBed
shortLabel GIAB SVs
longLabel Genome In a Bottle Structural Variants
group var
bigDataUrl https://hgdownload.soe.ucsc.edu/gbdb/hg38/giab/structuralVariants/giabSv.bb
html https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=giab

track dgvGold
type bigBed
shortLabel DGV Gold Standard
longLabel Database of Genomic Variants: Gold Structural Variants
group var
bigDataUrl https://hgdownload.soe.ucsc.edu/gbdb/hg38/dgv/dgvGold.bb
html https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38g=dgvPlus

track dgv
type bigBed
shortLabel DGV Struct Var
longLabel Database of Genomic Variants: Structural Var Regions
group var
bigDataUrl https://hgdownload.soe.ucsc.edu/gbdb/hg38/dgv/dgvMerged.bb
html https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38g=dgvPlus

track dgvSupp
type bigBed
shortLabel DGV Supp Var
longLabel Database of Genomic Variants: Supporting Structural Variants
group var
bigDataUrl https://hgdownload.soe.ucsc.edu/gbdb/hg38/dgv/dgvSupporting.bb
html https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38g=dgvPlus

track gnomExomes
type bigBed
shortLabel gnomAD Exome
longLabel Genome Aggregation Database (gnomAD) Exome Variants v4.1
group var
bigDataUrl https://hgdownload.soe.ucsc.edu/gbdb/hg38/gnomAD/v4.1/exomes/exomes.bb
html https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=gnomadVariants

track gnomExomes
type bigBed
shortLabel gnomAD Genome
longLabel Genome Aggregation Database (gnomAD) Genome Variants v4.1
group var
bigDataUrl https://hgdownload.soe.ucsc.edu/gbdb/hg38/gnomAD/v4.1/genomes/genomes.bb
html https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=gnomadVariants