be4311c07e14feb728abc6425ee606ffaa611a58 markd Fri Jan 22 06:46:58 2021 -0800 merge with master diff --git src/hg/makeDb/trackDb/human/trackDb.ra src/hg/makeDb/trackDb/human/trackDb.ra index 1d9e9fb..7acb248 100644 --- src/hg/makeDb/trackDb/human/trackDb.ra +++ src/hg/makeDb/trackDb/human/trackDb.ra @@ -20,30 +20,33 @@ # 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 +# CADD scores +include cadd.ra alpha + 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 + track hiSeqDepth @@ -119,31 +122,30 @@ visibility hide type bigBed 9 + itemRgb on tableBrowser off bigDataUrl /gbdb/$D/decipher/decipherCnv.bb url https://decipher.sanger.ac.uk/patient/$$ urlLabel Decipher Patient View: filter.size 0 filterByRange.size on filterLimits.size 2:170487333 filterValues.variant_class Amplification,Copy-Number Gain,Deletion,Duplication,Duplication/Trip filterValues.pathogenicity Benign,Likely Benign,Likely Pathogenic,Pathogenic,Uncertain,Unknown mergeSpannedItems on searchIndex name mouseOverField _mouseOver -pennantIcon Updated red ../goldenPath/newsarch.html#101320 "Updated Oct. 13, 2020" searchTable decipher searchMethod exact searchType bigBed release alpha,beta track decipherSnvs shortLabel DECIPHER SNVs longLabel DECIPHER: Chromosomal Imbalance and Phenotype in Humans (SNVs) group phenDis visibility hide color 0,0,0 type bed 4 tableBrowser off decipherSnvsRaw prevExonText Left edge @@ -188,50 +190,30 @@ track avada shortLabel Avada Variants longLabel Avada Variants extracted from full text publications visibility dense type bigBed 9 + bigDataUrl /gbdb/$D/bbi/avada.bb noScoreFilter on exonNumbers off #itemRgb on dataVersion release 1 parent varsInPubs pack urls pmid="https://www.ncbi.nlm.nih.gov/pubmed/$$" doi="https://doi.org/$$" ensId="http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?g=$$" entrezs="https://www.ncbi.nlm.nih.gov/gene/$$" refSeq="https://www.ncbi.nlm.nih.gov/nuccore/$$" mouseOverField _mouseOver -track pathoPred -type bigWig -longLabel Pathogenicity predictions -shortLabel Pathogenicity -color 112,172,192 -visibility hide -superTrack on -group phenDis - - track cadd - type bigWig - longLabel CADD scores version 1.4 - viewLimits 0:30 - color 100,130,160 - bigDataUrl /gbdb/$D/bbi/CADD-v1.4.bw - viewLimitsMax 0:100 - shortLabel CADD - visibility full - parent pathoPred on - track caseControl compositeTrack on shortLabel Case Control longLabel Case Control Consortium group phenDis visibility hide type chromGraph minMax 0,15 linesAt 5,10 track cccTrendPvalBd parent caseControl shortLabel CCC Bipolar Dis longLabel Case Control Consortium Bipolar Disorder Trend -log10 P-value priority 1 @@ -3158,78 +3140,78 @@ shortLabel sno/miRNA longLabel C/D and H/ACA Box snoRNAs, scaRNAs, and microRNAs from snoRNABase and miRBase group genes visibility hide color 200,80,0 type bed 8 + noScoreFilter . urlLabel Laboratoire de Biologie Moleculaire Eucaryote: url http://www-snorna.biotoul.fr/plus.php?id=$$ url2Label miRBase: #url2 http://microrna.sanger.ac.uk/cgi-bin/sequences/mirna_entry.pl?id=$$ url2 http://www.mirbase.org/cgi-bin/query.pl?terms=$$ dataVersion miRBase Release 13.0 (March 2009) and snoRNABase Version 3 track lrgBigPsl -shortLabel LRG Transcripts (RM 24672) -longLabel Locus Reference Genomic (LRG) Fixed Transcript Annotations (RedMine 24672) +shortLabel LRG Transcripts +longLabel Locus Reference Genomic (LRG) Fixed Transcript Annotations group genes visibility hide type bigPsl -mouseOverField mouseOver +html lrgTranscriptAli +mouseOver ${name}: ${ncbiTranscript} ${ensemblTranscript} ${ncbiProtein} ${ensemblProtein} ${geneName} skipFields mouseOver skipEmptyFields on urls ncbiTranscript=https://www.ncbi.nlm.nih.gov/nuccore/$$ 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=$$ -cdsTable lrgCds -cdnaTable lrgCdna -pepTable lrgPep altColor 127,127,127 baseColorDefault genomicCodons baseColorUseSequence lfExtra -baseColorUseCds table lrgCds indelDoubleInsert on indelPolyA on indelQueryInsert on showDiffBasesAllScales . showDiffBasesMaxZoom 10000.0 showCdsAllScales . showCdsMaxZoom 10000.0 color 54,125,29 urlLabel Link to LRG transcript: url http://ftp.ebi.ac.uk/pub/databases/lrgex/$$.xml#transcripts_anchor +bigDataUrl /gbdb/$D/bbi/lrgBigPsl.bb +release alpha 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 http://ftp.ebi.ac.uk/pub/databases/lrgex/$$.xml#transcripts_anchor +release beta,public track affyHuEx1 shortLabel Affy HuEx 1.0 longLabel Affymetrix Human Exon 1.0 Probe Sets group expression visibility hide url http://www.affymetrix.com/analysis/netaffx/exon/probe_set.affx?pk=1:$$ urlLabel Netaffx Link: useScore 1 type bed 6 . track affyHumanExon shortLabel Affy All Exon longLabel Affymetrix All Exon Chips group expression @@ -3689,31 +3671,30 @@ type bigBed 12 + release alpha bigDataUrl /gbdb/$D/bbi/cancerMutations/BRCA.bb urls case_id=https://portal.gdc.cancer.gov/cases/$$ parent cancerMutations track lovdComp shortLabel LOVD Variants longLabel Leiden Open Variation Database Public Variants group phenDis visibility hide compositeTrack on type bigBed 4 + tableBrowser off lovdComp html lovdComp -pennantIcon Updated red ../goldenPath/newsarch.html#101320 "Updated Oct. 13, 2020" track lovdShort shortLabel LOVD Variants < 50 bp longLabel Leiden Open Variation Database, short < 50 bp variants group phenDis visibility hide urls id="http://varcache.lovd.nl/redirect/$$" noScoreFilter on bigDataUrl /gbdb/$D/lovd/lovd.$D.short.bb parent lovdComp track lovdLong type bigBed 9 + shortLabel LOVD Variants >= 50 bp longLabel Leiden Open Variation Database Public Variants, long >= 50 bp variants @@ -3726,30 +3707,31 @@ mergeSpannedItems on track hgmd shortLabel HGMD Variants longLabel Human Gene Mutation Database Public Variants group phenDis visibility hide itemRgb on type bigBed 9 . url http://www.hgmd.cf.ac.uk/ac/gene.php?gene=$P&accession=$p urlLabel Link to HGMD mouseOverField variantType tableBrowser off hgmd noScoreFilter on maxItems 1000 +pennantIcon Updated red track snpedia shortLabel SNPedia longLabel SNPedia group phenDis visibility hide color 50,0,100 type bed 4 compositeTrack on track snpediaText parent snpedia shortLabel SNPedia with text longLabel SNPedia pages with manually typed text color 50,0,100 @@ -4064,36 +4046,45 @@ searchType bed termRegex Hs\.[0-9]+ searchPriority 20 searchTable uniGene_3 searchType psl termRegex Hs\.[0-9]+ searchPriority 20 searchTable HInvGeneMrna searchMethod exact searchType psl termRegex HIT[0-9]{9,9} searchPriority 50 +searchTable lrgBigPsl +searchMethod exact +searchType bigBed +termRegex LRG_[0-9]+t[0-9]+ +semiShortCircuit 1 +searchPriority 50 +release alpha + searchTable lrgTranscriptAli searchMethod exact searchType psl termRegex LRG_[0-9]+t[0-9]+ semiShortCircuit 1 searchPriority 50 +release beta,public searchName lrgTranscriptAliNoTNum searchTable lrgTranscriptAli query select tName, tStart, tEnd, qName from %s where qName like '%st%%' termRegex LRG_[0-9]+ dontCheck LRG_[0-9]+t[0-9+] semiShortCircuit 1 searchPriority 50 searchTable acescan searchMethod fuzzy searchType genePred termRegex .*_pred\.[0-9]+ searchPriority 50 @@ -5082,31 +5073,30 @@ include decode.rmap.ra #geneReviews track track geneReviews shortLabel GeneReviews longLabel GeneReviews group phenDis visibility hide color 0, 80, 0 type bigBed 9 + bigDataUrl /gbdb/$D/geneReviews/geneReviews.bb mouseOver $name disease(s): $diseases html geneReviews url https://www.ncbi.nlm.nih.gov/books/NBK1116/?term=$$ noScoreFilter on -pennantIcon Updated red ../goldenPath/newsarch.html#101320 "Updated Oct. 13, 2020" searchName geneReviews searchTable geneReviews searchType bed searchPriority 50 xrefTable geneReviewsDetail xrefQuery select geneSymbol,grTitle from %s where grTitle like '%%%s%%' searchBoth on searchTable dgv searchType bed searchPriority 50 termRegex (dgv_|[en]ss?v)[0-9]+ searchTable coriellDelDup