1eb62c61ee677b7a3c90cc77465dcbeacec479ce angie Tue Nov 5 13:30:58 2019 -0800 Oops, forgot to add some values to ucscNotesFilterValues. refs #23283 diff --git src/hg/makeDb/trackDb/human/trackDb.ra src/hg/makeDb/trackDb/human/trackDb.ra index b98d01c..24b4805 100644 --- src/hg/makeDb/trackDb/human/trackDb.ra +++ src/hg/makeDb/trackDb/human/trackDb.ra @@ -1619,48 +1619,52 @@ 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 \ + 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,\ - delMismatch|Deleted sequence mismatches genomic reference sequence,\ 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,\ 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,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