54452ec022a6073410955c04e110a1784f71fb57 angie Wed Nov 13 17:37:34 2019 -0800 dbSnp153: add new ucscNote otherMapErr for mappings with the same rs# as a mapping w/inconsistent SPDI in BadCoords/Map Err subtrack. refs #23283 diff --git src/hg/makeDb/trackDb/human/trackDb.ra src/hg/makeDb/trackDb/human/trackDb.ra index 76610d9..da1ad0f 100644 --- src/hg/makeDb/trackDb/human/trackDb.ra +++ src/hg/makeDb/trackDb/human/trackDb.ra @@ -1615,55 +1615,57 @@ 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 type bigBed 4 detailsTabUrls _dataOffset=/gbdb/hgFixed/dbSnp/dbSnp153Details.tab.gz group varRep visibility pack url https://www.ncbi.nlm.nih.gov/snp/$$ urlLabel dbSNP: +subGroup1 view Views variants=Variants errs=Mapping_Errors priority 0.8 track dbSnp153ViewVariants view variants parent dbSnp153Composite shortLabel Variants visibility pack 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 \ altIsAmbiguous|Alternate allele contains IUPAC ambiguous base(s),\ classMismatch|Variant class/type is inconsistent with allele sizes,\ clinvar|Present in ClinVar,\ clinvarBenign|ClinVar significance of benign and/or likely benign,\ clinvarConflicting|ClinVar includes both benign and pathogenic reports,\ clinvarPathogenic|ClinVar significance of pathogenic and/or likely pathogenic,\ 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,\ diffMajor|Different projects report different major alleles,\ freqIsAmbiguous|Frequency reported for allele with IUPAC ambiguous base(s),\ freqNotRefAlt|Reference genome allele is not major allele in at least one project,\ multiMap|Variant is placed in more than one genomic position,\ + otherMapErr|Another mapping of this variant has illegal coords (indel mapping error?),\ overlapDiffClass|Variant overlaps other variant(s) of different type/class,\ overlapSameClass|Variant overlaps other variant(s) of same type/class but different position,\ rareAll|MAF < 1% in all projects that report frequencies (or no frequency data),\ rareSome|MAF < 1% in at least one project that reports frequencies,\ refIsAmbiguous|Reference genome allele contains IUPAC ambiguous base(s),\ refIsMinor|Reference genome allele is minor allele in at least one project that reports frequencies,\ refIsRare|Reference genome allele frequency is <1% in at least one project,\ refIsSingleton|Reference genome frequency is 0 in all projects that report frequencies,\ refMismatch|Reference allele mismatches reference genome sequence,\ 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,\ @@ -1674,65 +1676,70 @@ 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 track dbSnp153Common parent dbSnp153ViewVariants on + subGroups view=variants 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 dbSnp153ViewVariants + subGroups view=variants 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 dbSnp153ViewVariants + subGroups view=variants 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 dbSnp153ViewVariants + subGroups view=variants shortLabel All dbSNP (153) longLabel All Short Genetic Variants from dbSNP Release 153 bigDataUrl /gbdb/$D/snp/dbSnp153.bb maxWindowToDraw 1000000 priority 4 track dbSnp153ViewErrs parent dbSnp153Composite view errs shortLabel Mapping Errors visibility pack track dbSnp153BadCoords parent dbSnp153ViewErrs + subGroups view=errs shortLabel Map Err dbSnp (153) longLabel Mappings with Inconsistent Coordinates from dbSNP 153 bigDataUrl /gbdb/$D/snp/dbSnp153BadCoords.bb type bigBed 4 priority 5 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 + @@ -5307,57 +5314,64 @@ padding 250 searchTable dbSnp152 searchMethod exact searchType bigBed semiShortCircuit 1 termRegex rs[0-9]+ searchPriority 12.949 padding 100 searchTable dbSnp153Common searchMethod exact searchType bigBed semiShortCircuit 1 termRegex rs[0-9]+ -searchPriority 12.945 +searchPriority 12.9450 padding 100 searchTable dbSnp153ClinVar searchMethod exact searchType bigBed semiShortCircuit 1 termRegex rs[0-9]+ -searchPriority 12.946 +searchPriority 12.9451 padding 100 searchTable dbSnp153 searchMethod exact searchType bigBed semiShortCircuit 1 termRegex rs[0-9]+ -searchPriority 12.947 +searchPriority 12.9452 padding 100 searchTable dbSnp153Mult searchMethod exact searchType bigBed semiShortCircuit 1 termRegex rs[0-9]+ -searchPriority 12.948 +searchPriority 12.9453 padding 100 +searchTable dbSnp153BadCoords +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 searchTable cnvDevDelayCase semiShortCircuit 1 termRegex nssv[0-9]+ searchType bed searchPriority 50