06d7be056190c14b85e71bc12523f18ea6815b5e markd Mon Dec 7 00:50:29 2020 -0800 BLAT mmap index support merge with master diff --git src/hg/makeDb/trackDb/human/trackDb.ra src/hg/makeDb/trackDb/human/trackDb.ra index 572ab78..18ca53f 100644 --- src/hg/makeDb/trackDb/human/trackDb.ra +++ src/hg/makeDb/trackDb/human/trackDb.ra @@ -18,31 +18,31 @@ include trackDb.gtex.ra # GeneHancer from Weizmann labs include trackDb.geneHancer.ra # NCBI ClinVar include trackDb.clinvar.ra # NCBI dbVar include trackDb.dbVar.ra # ClinGen include trackDb.clinGen.ra # Genome In a Bottle -include trackDb.giab.ra alpha +include trackDb.giab.ra track cytoBandIdeo shortLabel Chromosome Band (Ideogram) longLabel Chromosome Bands Localized by FISH Mapping Clones (for Ideogram) group map visibility dense type bed 4 + track cytoBand shortLabel Chromosome Band longLabel Chromosome Bands Localized by FISH Mapping Clones group map visibility hide type bed 4 + @@ -82,31 +82,31 @@ track hiSeqDepthTop10Pct parent hiSeqDepth shortLabel Top 0.10 Depth longLabel Top 0.10 of Read Depth Distribution priority 5 track lrg shortLabel LRG Regions longLabel Locus Reference Genomic (LRG) Sequences Mapped to $date Assembly group map visibility hide type bigBed 12 + noScoreFilter . urlLabel Link to LRG report: -url ftp://ftp.ebi.ac.uk/pub/databases/lrgex/$$.xml +url http://ftp.ebi.ac.uk/pub/databases/lrgex/$$.xml urls hgncId="https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:$$" ncbiAcc="https://www.ncbi.nlm.nih.gov/nuccore/$$" baseColorDefault diffBases baseColorUseSequence lrg indelDoubleInsert on indelQueryInsert on showDiffBasesAllScales . color 72,167,38 track gad shortLabel GAD View longLabel Genetic Association Studies of Complex Diseases and Disorders group phenDis visibility hide color 200,0,0 type bed 4 @@ -162,31 +162,31 @@ bigDataUrl /gbdb/$D/bbi/phegeni.bb urls studyId=https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=$$ geneId1=https://www.ncbi.nlm.nih.gov/gene/?term=$$%5Buid%5D geneId2=https://www.ncbi.nlm.nih.gov/gene/?term=$$%5Buid%5D analysisId=https://www.ncbi.nlm.nih.gov/projects/SNP/gViewer/gView.cgi?aid=$$ catalogId=https://www.ebi.ac.uk/gwas/search?query=$$ track varsInPubs shortLabel Variants in Papers longLabel Genetic Variants mentioned in scientific publications superTrack on group phenDis type bed 3 track mastermind shortLabel Mastermind Variants longLabel Genomenon Mastermind Variants extracted from full text publications visibility dense type bigBed 9 + - urls url=https://mastermind.genomenon.com/detail?disease=all%20diseases&$$ + urls url=$$ bigDataUrl /gbdb/$D/bbi/mastermind.bb noScoreFilter on exonNumbers off mouseOverField _mouseOver itemRgb on mmcnt1Filter 0 mmcnt2Filter 0 mmcnt3Filter 0 dataVersion /gbdb/$D/bbi/mastermindRelease.txt parent varsInPubs pack track avada shortLabel Avada Variants longLabel Avada Variants extracted from full text publications visibility dense @@ -3181,53 +3181,53 @@ urls ncbiTranscript=https://www.ncbi.nlm.nih.gov/nuccore/$$ ensemblTranscript=http://www.ensembl.org/Multi/Search/Results?site=ensembl_all;q=$$ ncbiProtein=https://www.ncbi.nlm.nih.gov/protein/$$ ensemblProtein=http://www.ensembl.org/Multi/Search/Results?site=ensembl_all;q=$$ cdsTable lrgCds cdnaTable lrgCdna pepTable lrgPep baseColorDefault diffCodons baseColorUseCds table lrgCds baseColorUseSequence table lrgCdna indelDoubleInsert on indelQueryInsert on showDiffBasesAllScales . showDiffBasesMaxZoom 10000.0 showCdsAllScales . showCdsMaxZoom 10000.0 color 54,125,29 urlLabel Link to LRG transcript: -url ftp://ftp.ebi.ac.uk/pub/databases/lrgex/$$.xml#transcripts_anchor +url http://ftp.ebi.ac.uk/pub/databases/lrgex/$$.xml#transcripts_anchor track lrgTranscriptAli shortLabel LRG Transcripts longLabel Locus Reference Genomic (LRG) Fixed Transcript Annotations group genes visibility hide type psl . cdsTable lrgCds cdnaTable lrgCdna pepTable lrgPep baseColorDefault diffCodons baseColorUseCds table lrgCds baseColorUseSequence table lrgCdna indelDoubleInsert on indelQueryInsert on showDiffBasesAllScales . showDiffBasesMaxZoom 10000.0 showCdsAllScales . showCdsMaxZoom 10000.0 color 54,125,29 urlLabel Link to LRG transcript: -url ftp://ftp.ebi.ac.uk/pub/databases/lrgex/$$.xml#transcripts_anchor +url http://ftp.ebi.ac.uk/pub/databases/lrgex/$$.xml#transcripts_anchor track affyHuEx1 shortLabel Affy HuEx 1.0 longLabel Affymetrix Human Exon 1.0 Probe Sets group expression visibility hide url http://www.affymetrix.com/analysis/netaffx/exon/probe_set.affx?pk=1:$$ urlLabel Netaffx Link: useScore 1 type bed 6 . track affyHumanExon shortLabel Affy All Exon longLabel Affymetrix All Exon Chips group expression @@ -3616,53 +3616,30 @@ url http://www.omim.org/entry/ tableBrowser noGenome noGenomeReason Distribution restrictions by OMIM. See the track documentation for details. You can download the complete OMIM dataset for free from omim.org track omimGene2 shortLabel OMIM Genes longLabel OMIM Gene Phenotypes - Dark Green Can Be Disease-causing group phenDis visibility hide color 0, 80, 0 type bed 4 hgsid on url http://www.omim.org/entry/ tableBrowser noGenome omimGeneMap omimGeneMap2 omimPhenotype omimGeneSymbol omim2gene noGenomeReason Distribution restrictions by OMIM. See the track documentation for details. You can download the complete OMIM dataset for free from omim.org -release public - -track omimGene2bb -shortLabel OMIM Genes (New) -longLabel OMIM Gene Phenotypes - Dark Green Can Be Disease-causing -group phenDis -visibility hide -color 0, 80, 0 -type bigBed 9 + -hgsid on -url http://www.omim.org/entry/$$ -urlLabel Link to OMIM: -tableBrowser noGenome omimGeneMap omimGeneMap2 omimPhenotype omimGeneSymbol omim2gene -bigDataUrl /gbdb/$D/bbi/omimGene2.bb -itemRgb on -mouseOverField _mouseOver -noScoreFilter on -labelFields name,mainSym -defaultLabelFields name,mainSym -html omimGene2 -noGenomeReason Distribution restrictions by OMIM. See the track documentation for details. You can download the complete OMIM dataset for free from omim.org -release alpha,beta -searchIndex name track omimAvSnp shortLabel OMIM Alleles longLabel OMIM Allelic Variant Phenotypes group phenDis visibility hide color 0, 80, 0 type bed 4 hgsid on url http://www.omim.org/entry/ tableBrowser noGenome omimAv omimAvRepl noGenomeReason Distribution restrictions by OMIM. See the track documentation for details. You can download the complete OMIM dataset for free from omim.org track cosmic shortLabel COSMIC @@ -5460,46 +5437,49 @@ searchMethod exact searchType bigBed semiShortCircuit 1 termRegex rs[0-9]+ searchPriority 12.9454 padding 100 include cloneEnd.trackDb.ra track spMut override bigDataUrl /gbdb/$D/uniprot/unipMut.bb track sgpGene override longLabel SGP Gene Predictions Using Mouse/$Organism Homology +track uniprot override +hideEmptySubtracks off + searchTable cnvDevDelayCase semiShortCircuit 1 termRegex nssv[0-9]+ searchType bed searchPriority 50 searchTable cnvDevDelayControl semiShortCircuit 1 termRegex nssv[0-9]+ searchType bed searchPriority 50 include covidHgiGwas.ra -track covidHgeMuts +track covidMuts type bigBed 12 + -shortLabel COVID-19 Immunity Variants -longLabel COVID-19 Immunity Variants from the COVID Human Genetics Effort -mouseOver $name $rsId $gene Genotype: $genotype; Zygosity: $zygo ; Inheritance: $inhMode +shortLabel Rare Harmful Vars +longLabel Rare variants underlying COVID-19 severity and susceptibility from the COVID Human Genetics Effort +mouseOver $gene $name $rsId Genotype: $genotype; Zygosity: $zygo ; Inheritance: $inhMode labelFields gene, name defaultLabelFields gene, name noScoreFilter on group covid color 179,0,0 visibility hide -html covidHgeMuts -bigDataUrl /gbdb/hg38/covid/covidMuts.bb +bigDataUrl /gbdb/$D/covidMuts/covidMuts.bb +pennantIcon New red ../goldenPath/newsarch.html "Released Nov. 12, 2020"