b49e61be4ad54a46e01be904fa8a8985e9850f0d angie Tue Nov 12 12:27:30 2019 -0800 dbSnp153: add a bigBed4 subtrack of coordinate ranges for mappings that we dropped due to inconsistent SPDI. refs #23283 Overall counts increased because we used to bail on an entire variant when we discovered an inconsistent SPDI, losing some valid mappings. Now we go through all mappings, and the bad ones are stored instead of dropped. diff --git src/hg/makeDb/trackDb/human/trackDb.ra src/hg/makeDb/trackDb/human/trackDb.ra index 589a28e..76610d9 100644 --- src/hg/makeDb/trackDb/human/trackDb.ra +++ src/hg/makeDb/trackDb/human/trackDb.ra @@ -1609,98 +1609,136 @@ 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 +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: +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,\ 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 + 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 + parent dbSnp153ViewVariants 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 + parent dbSnp153ViewVariants 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 + parent dbSnp153ViewVariants 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 + parent dbSnp153ViewVariants 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 + 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 + 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,