767e3f123a734a5c0623b2e635c7cdc59e9fb61f braney Mon Mar 13 10:48:38 2023 -0700 starting on work to purge recommend track sets of all that is not relevant to the rts diff --git src/hg/utils/rts/hg38/Non_Coding_SNVs_hg38 src/hg/utils/rts/hg38/Non_Coding_SNVs_hg38 new file mode 100644 index 0000000..133087c --- /dev/null +++ src/hg/utils/rts/hg38/Non_Coding_SNVs_hg38 @@ -0,0 +1,353 @@ +European=Server%3C%2Fli%3E +_=1646762307890 +affyGnf1h=pack +affyU133=pack +affyU95=pack +altSeqLiftOverPsl=hide +augustusGene=pack +bismap=full +bloodHaoCellType=pack +brainDevRegionsTissueCellType=hide +c=chrX +cadd=full +caddA_imgOrd=17 +caddC_imgOrd=18 +caddDel=pack +caddDel_imgOrd=21 +caddG_imgOrd=19 +caddIns=pack +caddIns_imgOrd=22 +caddSuper=show +caddT_imgOrd=20 +cartVersion=2 +centerLabels=1 +clade=mammal +clinGenGeneDisease_imgOrd=9 +clinGenHaplo_imgOrd=7 +clinGenTriplo_imgOrd=8 +clinvar=pack +clinvarCnv.doMergeItems=1 +clinvarCnv_sel=0 +clinvarMain_imgOrd=11 +clinvarMain_sel=0 +clinvarSubLolly_imgOrd=10 +colonWangCellType=pack +cons100way=full +cons100wayViewalign.showCfg=off +cons100wayViewalign=hide +cons100wayViewelements.showCfg=off +cons100wayViewelements=dense +cons100wayViewphastcons.showCfg=off +cons100wayViewphastcons=full +cons100wayViewphyloP.showCfg=off +cortexVelmeshevCellType=pack +cpgIslandExt=pack +crispr10KRanges=hide +crispr10KTargets=hide +crisprEnsembl=hide +crisprKmers=hide +crisprRanges=hide +crisprTargets=hide +crossMatchUnique=hide +cytoBandIdeo=dense +db=hg38 +dbSnp153=dense +dbSnp153BadCoords_sel=%2D2 +dbSnp153Common_imgOrd=23 +dbSnp153Common_sel=0 +dbSnp153Composite=full +dbSnp153ViewErrs=hide +dbSnp153ViewVariants.showCfg=on +dbSnp153ViewVariants=dense +dbSnp153_imgOrd=12 +dbSnp153_sel=1 +dbVar_common=pack +dbVar_conflict=pack +defaultsSet=on +dinkL=2.0 +dinkR=2.0 +displaySubtracks=all +enableHighlightingDialog=1 +encodeCcreCombined.alwaysZero=OFF +encodeCcreCombined.autoScale=auto%2Dscale+to+data+view +encodeCcreCombined.doWiggle=0 +encodeCcreCombined.filterBy.ucscLabel=All +encodeCcreCombined.heightPer=128 +encodeCcreCombined.horizGrid=OFF +encodeCcreCombined.label.accessionLabel=1 +encodeCcreCombined.label.encodeLabel=0 +encodeCcreCombined.label.ucscLabel=1 +encodeCcreCombined.lineBar=bar +encodeCcreCombined.negateValues=0 +encodeCcreCombined.smoothingWindow=OFF +encodeCcreCombined.transformFunc=NONE +encodeCcreCombined.windowingFunction=maximum +encodeCcreCombined.yLineMark=0 +encodeCcreCombined.yLineOnOff=OFF +encodeCcreCombined=pack +encodeCcreCombined_imgOrd=26 +exonNumbers=1 +expOrder_caddSuper=caddG+caddC+caddT+caddA+ +expOrder_cons100way=phastCons100way+phyloP100way+ +expOrder_revel=revelC+revelG+revelA+revelT+ +expOrder_wgEncodeReg=wgEncodeRegDnaseWig+wgEncodeRegMarkH3k4me1+wgEncodeRegMarkH3k4me3+wgEncodeRegMarkH3k27ac+ +fetalGeneAtlasCellType=pack +fixSeqLiftOverPsl=hide +g=cons100way +g=cons100way +geneHancer=pack +geneHancerClusteredInteractionsDoubleElite_imgOrd=27 +geneHancerGenesDoubleElite_imgOrd=24 +geneHancerInteractionsDoubleElite_imgOrd=25 +geneHancerInteractionsDoubleElite_sel=1 +geneHancerRegElementsDoubleElite_imgOrd=23 +geneReviews=pack +geneReviews_imgOrd=6 +ghClusteredInteraction.showCfg=off +ghGeneHancer.showCfg=off +ghInteraction.heightPer=50 +ghInteraction.showCfg=off +ghInteraction=pack +gnomadGenomesVariantsV3_1_1.alwaysZero=OFF +gnomadGenomesVariantsV3_1_1.autoScale=auto%2Dscale+to+data+view +gnomadGenomesVariantsV3_1_1.doWiggle=0 +gnomadGenomesVariantsV3_1_1.filter.AF=0 +gnomadGenomesVariantsV3_1_1.filterBy.FILTER=PASS +gnomadGenomesVariantsV3_1_1.filterBy.annot=All +gnomadGenomesVariantsV3_1_1.filterBy.variation_type=All +gnomadGenomesVariantsV3_1_1.filterType.FILTER=multipleListAnd +gnomadGenomesVariantsV3_1_1.filterType.variation_type=multipleListOr +gnomadGenomesVariantsV3_1_1.heightPer=128 +gnomadGenomesVariantsV3_1_1.horizGrid=OFF +gnomadGenomesVariantsV3_1_1.label._displayName=1 +gnomadGenomesVariantsV3_1_1.label.rsId=0 +gnomadGenomesVariantsV3_1_1.lineBar=bar +gnomadGenomesVariantsV3_1_1.negateValues=0 +gnomadGenomesVariantsV3_1_1.section_superDescription_close=1 +gnomadGenomesVariantsV3_1_1.section_superMembers_close=0 +gnomadGenomesVariantsV3_1_1.smoothingWindow=OFF +gnomadGenomesVariantsV3_1_1.transformFunc=NONE +gnomadGenomesVariantsV3_1_1.windowingFunction=maximum +gnomadGenomesVariantsV3_1_1.yLineMark=0 +gnomadGenomesVariantsV3_1_1.yLineOnOff=OFF +gnomadGenomesVariantsV3_1_1=dense +gnomadGenomesVariantsV3_1_1_imgOrd=13 +gnomadVariants=show +goButton=go +gtexEqtlHighConf.dashes=1 +gtexEqtlHighConf.draw=curve +gtexEqtlHighConf.endsVisible=any +gtexEqtlHighConf.filter.cpp=0 +gtexEqtlHighConf.filterBy.tissue=Whole_Blood +gtexEqtlHighConf.filterText.geneName=%2A +gtexEqtlHighConf.filterType.geneName=wildcard +gtexEqtlHighConf.heightPer=200 +gtexEqtlHighConf=pack +gtexEqtlHighConf_imgOrd=43 +gtexGeneV8=hide +gtexGeneV8_imgOrd=35 +guidelines=1 +heartAtlasCellTypes=pack +hgFind.matches=ENST00000678073.1%2C +hgPS_DataTableState=%257B%2522time%2522%253A1602591005253%252C%2522start%2522%253A0%252C%2522length%2522%253A10%252C%2522order%2522%253A%255B%255B2%252C%2522desc%2522%255D%255D%252C%2522search%2522%253A%257B%2522search%2522%253A%2522%2522%252C%2522smart%2522%253Atrue%252C%2522regex%2522%253Afalse%252C%2522caseInsensitive%2522%253Atrue%257D%252C%2522columns%2522%253A%255B%257B%2522visible%2522%253Atrue%252C%2522search%2522%253A%257B%2522search%2522%253A%2522%2522%252C%2522smart%2522%253Atrue%252C%2522regex%2522%253Afalse%252C%2522caseInsensitive%2522%253Atrue%257D%257D%252C%257B%2522visible%2522%253Atrue%252C%2522search%2522%253A%257B%2522search%2522%253A%2522%2522%252C%2522smart%2522%253Atrue%252C%2522regex%2522%253Afalse%252C%2522caseInsensitive%2522%253Atrue%257D%257D%252C%257B%2522visible%2522%253Afalse%252C%2522search%2522%253A%257B%2522search%2522%253A%2522%2522%252C%2522smart%2522%253Atrue%252C%2522regex%2522%253Afalse%252C%2522caseInsensitive%2522%253Atrue%257D%257D%252C%257B%2522visible%2522%253Afalse%252C%2522search%2522%253A%257B%2522search%2522%253A%2522%2522%252C%2522smart%2522%253Atrue%252C%2522regex%2522%253Afalse%252C%2522caseInsensitive%2522%253Atrue%257D%257D%255D%257D +hgPS_DataTableState=%257B%2522time%2522%253A1602591005253%252C%2522start%2522%253A0%252C%2522length%2522%253A10%252C%2522order%2522%253A%255B%255B2%252C%2522desc%2522%255D%255D%252C%2522search%2522%253A%257B%2522search%2522%253A%2522%2522%252C%2522smart%2522%253Atrue%252C%2522regex%2522%253Afalse%252C%2522caseInsensitive%2522%253Atrue%257D%252C%2522columns%2522%253A%255B%257B%2522visible%2522%253Atrue%252C%2522search%2522%253A%257B%2522search%2522%253A%2522%2522%252C%2522smart%2522%253Atrue%252C%2522regex%2522%253Afalse%252C%2522caseInsensitive%2522%253Atrue%257D%257D%252C%257B%2522visible%2522%253Atrue%252C%2522search%2522%253A%257B%2522search%2522%253A%2522%2522%252C%2522smart%2522%253Atrue%252C%2522regex%2522%253Afalse%252C%2522caseInsensitive%2522%253Atrue%257D%257D%252C%257B%2522visible%2522%253Afalse%252C%2522search%2522%253A%257B%2522search%2522%253A%2522%2522%252C%2522smart%2522%253Atrue%252C%2522regex%2522%253Afalse%252C%2522caseInsensitive%2522%253Atrue%257D%257D%252C%257B%2522visible%2522%253Afalse%252C%2522search%2522%253A%257B%2522search%2522%253A%2522%2522%252C%2522smart%2522%253Atrue%252C%2522regex%2522%253Afalse%252C%2522caseInsensitive%2522%253Atrue%257D%257D%255D%257D +hgS_DataTableState=%257B%2522time%2522%253A1647463522856%252C%2522start%2522%253A0%252C%2522length%2522%253A10%252C%2522order%2522%253A%255B2%252C%2522desc%2522%255D%252C%2522search%2522%253A%257B%2522search%2522%253A%2522%2522%252C%2522smart%2522%253Atrue%252C%2522regex%2522%253Afalse%252C%2522caseInsensitive%2522%253Atrue%257D%252C%2522columns%2522%253A%255B%257B%2522visible%2522%253Atrue%252C%2522search%2522%253A%257B%2522search%2522%253A%2522%2522%252C%2522smart%2522%253Atrue%252C%2522regex%2522%253Afalse%252C%2522caseInsensitive%2522%253Atrue%257D%257D%252C%257B%2522visible%2522%253Atrue%252C%2522search%2522%253A%257B%2522search%2522%253A%2522%2522%252C%2522smart%2522%253Atrue%252C%2522regex%2522%253Afalse%252C%2522caseInsensitive%2522%253Atrue%257D%257D%252C%257B%2522visible%2522%253Atrue%252C%2522search%2522%253A%257B%2522search%2522%253A%2522%2522%252C%2522smart%2522%253Atrue%252C%2522regex%2522%253Afalse%252C%2522caseInsensitive%2522%253Atrue%257D%257D%252C%257B%2522visible%2522%253Atrue%252C%2522search%2522%253A%257B%2522search%2522%253A%2522%2522%252C%2522smart%2522%253Atrue%252C%2522regex%2522%253Afalse%252C%2522caseInsensitive%2522%253Atrue%257D%257D%252C%257B%2522visible%2522%253Atrue%252C%2522search%2522%253A%257B%2522search%2522%253A%2522%2522%252C%2522smart%2522%253Atrue%252C%2522regex%2522%253Afalse%252C%2522caseInsensitive%2522%253Atrue%257D%257D%252C%257B%2522visible%2522%253Atrue%252C%2522search%2522%253A%257B%2522search%2522%253A%2522%2522%252C%2522smart%2522%253Atrue%252C%2522regex%2522%253Afalse%252C%2522caseInsensitive%2522%253Atrue%257D%257D%252C%257B%2522visible%2522%253Atrue%252C%2522search%2522%253A%257B%2522search%2522%253A%2522%2522%252C%2522smart%2522%253Atrue%252C%2522regex%2522%253Afalse%252C%2522caseInsensitive%2522%253Atrue%257D%257D%252C%257B%2522visible%2522%253Atrue%252C%2522search%2522%253A%257B%2522search%2522%253A%2522%2522%252C%2522smart%2522%253Atrue%252C%2522regex%2522%253Afalse%252C%2522caseInsensitive%2522%253Atrue%257D%257D%252C%257B%2522visible%2522%253Atrue%252C%2522search%2522%253A%257B%2522search%2522%253A%2522%2522%252C%2522smart%2522%253Atrue%252C%2522regex%2522%253Afalse%252C%2522caseInsensitive%2522%253Atrue%257D%257D%255D%257D +hgS_loadUrlName= +hgS_newSessionName=Non_Coding_SNVs_hg38 +hgS_newSessionShare=1 +hgS_otherUserName= +hgS_otherUserSessionName= +hgS_saveLocalFileCompress=none +hgS_saveLocalFileName= +hgmd=pack +hgmd_imgOrd=8 +hgt.labelWidth=20 +hgtgroup_compGeno_close=0 +hgtgroup_covid_close=1 +hgtgroup_expression_close=1 +hgtgroup_genes_close=0 +hgtgroup_map_close=1 +hgtgroup_phenDis_close=0 +hgtgroup_regulation_close=0 +hgtgroup_rep_close=0 +hgtgroup_rna_close=1 +hgtgroup_singleCell_close=1 +hgtgroup_varRep_close=0 +highlight=hg38%23chr11%235227002%235227002%23d8f7d7 +hippocampusAyhanCellType=hide +hmmerUnique=hide +ideogram=1 +ileumWangCellType=pack +jaspar2022_imgOrd=31 +jaspar=dense +jsh_pageVertPos=0 +kidneyStewartCellType=pack +knownGene=hide +knownGeneV36=hide +knownGeneV38=hide +knownGene_imgOrd=38 +l=15557038 +lastPosition=chrX%3A15557039%2D15607236 +lastVirtModeExtraState= +lastVirtModeType=default +leftLabels=1 +lincRNAsAllCellTypeTopView=dense +lincRNAsTranscripts=pack +liverMacParlandCellType=pack +lovdComp=pack +lovdLong.doMergeItems=1 +lovdLong_imgOrd=29 +lovdLong_sel=0 +lovdShort_imgOrd=9 +lrgTranscriptAli=pack +lrgTranscriptAli_imgOrd=3 +lungTravaglini2020CellType10x=pack +mane=pack +mane_imgOrd=4 +mastermind=dense +mastermind_imgOrd=11 +multiz100way_imgOrd=26 +multiz100way_sel=%2D1 +muscleDeMicheliCellType=pack +ncbiAltMappingsChain=hide +ncbiAltMappingsMaf=hide +ncbiRefSeqCurated_imgOrd=1 +ncbiRefSeqHgmd_imgOrd=2 +ncbiRefSeqHgmd_sel=1 +nextExonArrows=1 +nextItemArrows=0 +o=15564569 +oldPosition=chrX%3A15557039%2D15607236 +omimAvSnp=hide +omimGene2.label.class1=1 +omimGene2.label.class2=1 +omimGene2.label.class3=1 +omimGene2.label.class4=1 +omimGene2.label.gene=1 +omimGene2.label.omimId=1 +omimGene2.label.others=1 +omimGene2=pack +omimGene2_imgOrd=5 +oreganno.filter.haplo=1 +oreganno.filter.mirna=1 +oreganno.filter.poly=1 +oreganno.filter.reg=1 +oreganno.filter.tfbs=1 +oreganno_imgOrd=26 +org=Human +orphadata=pack +orphadata_imgOrd=7 +pancreasBaronCellType=pack +phastCons100way_imgOrd=15 +phastCons100way_sel=1 +phastConsElements100way_imgOrd=16 +phastConsElements100way_sel=1 +phyloP100way_imgOrd=14 +phyloP100way_sel=1 +pix=1779 +placentaVentoTormoCellType10x=pack +placentaVentoTormoLocation10x=pack +placentaVentoTormoLocationSs2=pack +position.hg38=lastVirtModeType%3Ddefault%26lastVirtModeExtraState%3D%26virtModeType%3Ddefault%26virtMode%3D0%26nonVirtPosition%3D%26position%3DchrX%253A15557039%252D15607236 +position=chrX%3A15557039%2D15607236 +quakeGeneExpr=hide +r=15607236 +rectumWangCellType=pack +redirect=manual +refSeqComposite.label.gene=1 +refSeqComposite=pack +revelA_imgOrd=34 +revelC_imgOrd=35 +revelG_imgOrd=36 +revelT_imgOrd=37 +rmsk=hide +rmskBlastn=hide +rmskCM=hide +rmskGenbank=hide +rmskHmmer2020=hide +rmskHmmer=hide +rmsk_imgOrd=25 +ruler=dense +sessionTable_length=10 +simOrder_caddSuper=caddA+caddG+caddC+caddT+ +simOrder_cons100way=phastCons100way+phyloP100way+ +simOrder_revel=revelG+revelA+revelC+revelT+ +simOrder_wgEncodeReg=wgEncodeRegDnaseWig+wgEncodeRegMarkH3k27ac+wgEncodeRegMarkH3k4me1+wgEncodeRegMarkH3k4me3+ +skinSoleBoldoCellType=pack +snp151Common=pack +spMut.alwaysZero=OFF +spMut.autoScale=auto%2Dscale+to+data+view +spMut.doWiggle=0 +spMut.heightPer=128 +spMut.horizGrid=OFF +spMut.lineBar=bar +spMut.negateValues=0 +spMut.smoothingWindow=OFF +spMut.transformFunc=NONE +spMut.windowingFunction=maximum +spMut.yLineMark=0 +spMut.yLineOnOff=OFF +spMut_imgOrd=15 +t=15564570 +tRNAs=pack +tabulaSapiensTissueCellType=hide +tcgaGeneExpr=pack +tcgaTranscExpr=pack +textFont=Helvetica +textSize=12 +textStyle=Normal +tgpTrios=hide +toothKrivanekTissueCellType=hide +topSubmit=submit +trackControlsOnMain=1 +trackHubs= +transMapEnsemblV4=hide +transMapEnsemblV5=pack +transMapEnsemblV6=hide +transMapRefSeqV4=hide +transMapRefSeqV5=pack +transMapRefSeqV6=hide +transMapRnaV4=hide +umap=full +unipAliSwissprot_sel=0 +unipChain_sel=0 +unipDisulfBond_imgOrd=24 +unipDomain_imgOrd=23 +unipFullSeq_sel=0 +unipInterest_imgOrd=19 +unipLocCytopl_imgOrd=22 +unipLocExtra_imgOrd=20 +unipLocSignal_imgOrd=18 +unipLocTransMemb_imgOrd=21 +unipModif_imgOrd=25 +unipMut_sel=0 +unipOther_sel=0 +unipRepeat_sel=0 +unipStruct_sel=0 +varsInPubs=show +virtMode=0 +virtModeType=default +wgEncodeGencodeV38=pack +wgEncodeGencodeV39=hide +wgEncodeReg=hide +wgEncodeRegDnase=pack +wgEncodeRegDnaseClustered=pack +wgEncodeRegDnaseClustered_imgOrd=32 +wgEncodeRegDnaseUwGm12878Peak_imgOrd=40 +wgEncodeRegDnaseUwH7hescPeak_imgOrd=41 +wgEncodeRegDnaseUwHelas3Peak_imgOrd=42 +wgEncodeRegDnaseUwHepg2Peak_imgOrd=39 +wgEncodeRegDnaseUwHsmmPeak_imgOrd=36 +wgEncodeRegDnaseUwHuvecPeak_imgOrd=37 +wgEncodeRegDnaseUwK562Peak_imgOrd=34 +wgEncodeRegDnaseUwNhekPeak_imgOrd=38 +wgEncodeRegDnaseUwNhlfPeak_imgOrd=35 +wgEncodeRegDnaseWig=pack +wgEncodeRegDnaseWig_imgOrd=33 +wgEncodeRegMarkH3k27ac=pack +wgEncodeRegMarkH3k27ac_imgOrd=29 +wgEncodeRegMarkH3k4me1=pack +wgEncodeRegMarkH3k4me1_imgOrd=28 +wgEncodeRegMarkH3k4me3=pack +wgEncodeRegMarkH3k4me3_imgOrd=30 +wgRna=pack