895644af226dd57285d4b0469da87dc34df76e5e angie Thu Oct 24 13:55:25 2019 -0700 trackDb and descriptions for new tracks dbSnp152* and dbSnp153*. tagTypes changes for bigDbSnp type (and subsequent big* types). refs #23283 diff --git src/hg/makeDb/trackDb/human/trackDb.ra src/hg/makeDb/trackDb/human/trackDb.ra index 963120c..8f9edb0 100644 --- src/hg/makeDb/trackDb/human/trackDb.ra +++ src/hg/makeDb/trackDb/human/trackDb.ra @@ -1584,30 +1584,99 @@ visibility hide url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$ urlLabel dbSNP: defaultGeneTracks knownGene maxWindowToDraw 10000000 type bed 6 + trackHandler snp125 chimpOrangMacOrthoTable snp151OrthoPt5Pa2Rm8 chimpDb panTro5 orangDb ponAbe2 macaqueDb rheMac8 hapmapPhase III codingAnnotations snp151CodingDbSnp, priority 6.9 +track dbSnp152 +shortLabel All dbSNP (152) +longLabel Short Genetic Variants from dbSNP release 152 +bigDataUrl /gbdb/$D/snp/dbSnp152.bb +detailsTabUrls _dataOffset=/gbdb/hgFixed/dbSnp/dbSnp152Details.tab.gz +group varRep +visibility dense +url https://www.ncbi.nlm.nih.gov/snp/$$ +urlLabel dbSNP: +type bigDbSnp +freqSourceOrder 1000Genomes,GnomAD_exomes,TOPMED,GnomAD,ExAC,GoESP,ALSPAC,TWINSUK,Estonian +maxWindowToDraw 1000000 +classFilterValues snv,mnv,ins,del,delins,identity +classFilterType multipleListOr +ucscNotesFilterValues |(nothing noted),classMismatch|Variant class/type is inconsistent with allele sizes,clinvar|Present in ClinVar,clusterError|Overlaps a variant with the same type/class and position,commonAll|MAF >= 1% in all projects that report frequencies,commonSome|MAF >= 1% in at least one project that reports frequencies,delMismatch|Deleted sequence mismatches genomic reference sequence,diffMajor|Different projects report different major alleles,multiMap|Variant is placed in more than one genomic position,overlapDiffClass|Variant overlaps other variant(s) of different type/class,overlapSameClass|Variant overlaps other variant(s) of same type/class but different position,refIsMinor|Genomic reference allele is minor allele in at least one project that reports frequencies,refIsRare|Genomic reference allele frequency is <1% in at least one project,refIsSingleton|Genomic reference frequency is 0 in all projects reporting frequencies,revStrand|Variant maps to opposite strand relative to dbSNP's preferred top-level placement +ucscNotesFilterType multipleListOr +maxFuncImpactFilterValues 0|(not annotated),0865|frameshift,1587|stop_gained,1574|splice_acceptor_variant,1575|splice_donor_variant,1821|inframe_insertion,1583|missense_variant,1590|terminator_codon_variant,1819|synonymous_variant,1580|coding_sequence_variant,1623|5_prime_UTR_variant,1624|3_prime_UTR_variant,1619|nc_transcript_variant,2153|genic_upstream_transcript_variant,1986|upstream_transcript_variant,2152|genic_downstream_transcript_variant,1987|downstream_transcript_variant,1627|intron_variant +maxFuncImpactFilterType multipleListOr +priority 6.8 + +track dbSnp153Composite +compositeTrack on +shortLabel dbSNP 153 +longLabel Short Genetic Variants from dbSNP release 153 +detailsTabUrls _dataOffset=/gbdb/hgFixed/dbSnp/dbSnp153Details.tab.gz +group varRep +visibility pack +url https://www.ncbi.nlm.nih.gov/snp/$$ +urlLabel dbSNP: +type bigDbSnp +freqSourceOrder 1000Genomes,GnomAD_exomes,TOPMED,ExAC,PAGE_STUDY,GnomAD,GoESP,Estonian,ALSPAC,TWINSUK,NorthernSweden,Vietnamese +classFilterValues snv,mnv,ins,del,delins,identity +classFilterType multipleListOr +ucscNotesFilterValues |(nothing noted),classMismatch|Variant class/type is inconsistent with allele sizes,clinvar|Present in ClinVar,clusterError|Overlaps a variant with the same type/class and position,commonAll|MAF >= 1% in all projects that report frequencies,commonSome|MAF >= 1% in at least one project that reports frequencies,delMismatch|Deleted sequence mismatches genomic reference sequence,diffMajor|Different projects report different major alleles,multiMap|Variant is placed in more than one genomic position,overlapDiffClass|Variant overlaps other variant(s) of different type/class,overlapSameClass|Variant overlaps other variant(s) of same type/class but different position,refIsMinor|Genomic reference allele is minor allele in at least one project that reports frequencies,refIsRare|Genomic reference allele frequency is <1% in at least one project,refIsSingleton|Genomic reference frequency is 0 in all projects reporting frequencies,revStrand|Variant maps to opposite strand relative to dbSNP's preferred top-level placement +#' +ucscNotesFilterType multipleListOr +maxFuncImpactFilterValues 0|(not annotated),0865|frameshift,1587|stop_gained,1574|splice_acceptor_variant,1575|splice_donor_variant,1821|inframe_insertion,1583|missense_variant,1590|terminator_codon_variant,1819|synonymous_variant,1580|coding_sequence_variant,1623|5_prime_UTR_variant,1624|3_prime_UTR_variant,1619|nc_transcript_variant,2153|genic_upstream_transcript_variant,1986|upstream_transcript_variant,2152|genic_downstream_transcript_variant,1987|downstream_transcript_variant,1627|intron_variant +maxFuncImpactFilterType multipleListOr +priority 0.8 + + track dbSnp153Common + parent dbSnp153Composite on + shortLabel Common dbSNP (153) + longLabel Common (1000 Genomes Phase 3 MAF >= 1%) Short Genetic Variants from dbSNP Release 153 + bigDataUrl /gbdb/$D/snp/dbSnp153Common.bb + priority 1 + + track dbSnp153ClinVar + parent dbSnp153Composite + shortLabel ClinVar dbSNP (153) + longLabel Short Genetic Variants from dbSNP Release 153 Included in ClinVar + bigDataUrl /gbdb/$D/snp/dbSnp153ClinVar.bb + priority 2 + + track dbSnp153Mult + parent dbSnp153Composite + shortLabel Mult. dbSNP (153) + longLabel Short Genetic Variants from dbSNP Release 153 That Map to Multiple Genomic Loci + bigDataUrl /gbdb/$D/snp/dbSnp153Mult.bb + priority 3 + + track dbSnp153 + parent dbSnp153Composite + shortLabel All dbSNP (153) + longLabel All Short Genetic Variants from dbSNP Release 153 + bigDataUrl /gbdb/$D/snp/dbSnp153.bb + maxWindowToDraw 1000000 + priority 4 + track hgdpGeo shortLabel HGDP Allele Freq longLabel Human Genome Diversity Project SNP Population Allele Frequencies group varRep visibility hide url http://hgdp.uchicago.edu/cgi-bin/gbrowse/HGDP/?name=$$ urlLabel HGDP Selection Browser: type bed 4 + track hgdpFst shortLabel HGDP Smoothd FST longLabel Human Genome Diversity Project Smoothed Relative FST (Fixation Index) group varRep visibility hide chromosomes chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22, @@ -5126,30 +5195,47 @@ searchMethod exact searchType bed semiShortCircuit 1 termRegex rs[0-9]+ searchPriority 12.9839 padding 250 searchTable snp151 searchMethod exact searchType bed semiShortCircuit 1 termRegex rs[0-9]+ searchPriority 12.950 padding 250 +searchTable dbSnp152 +searchMethod exact +searchType bigBed +semiShortCircuit 1 +termRegex rs[0-9]+ +searchPriority 12.949 +padding 100 + +searchTable dbSnp153 +searchMethod exact +searchType bigBed +semiShortCircuit 1 +termRegex rs[0-9]+ +searchPriority 12.948 +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 searchTable cnvDevDelayCase semiShortCircuit 1 termRegex nssv[0-9]+ searchType bed searchPriority 50 searchTable cnvDevDelayControl