2eaedbb507227d834dd9fc191bc029a140809974 lrnassar Fri Oct 7 16:50:12 2022 -0700 Adding maxWindowCov to make dbSnp density graph and tweaking cfg for more clarity, refs #29715 diff --git src/hg/makeDb/trackDb/human/trackDb.ra src/hg/makeDb/trackDb/human/trackDb.ra index 6eb4101..76b5322 100644 --- src/hg/makeDb/trackDb/human/trackDb.ra +++ src/hg/makeDb/trackDb/human/trackDb.ra @@ -1632,30 +1632,31 @@ #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 #release alpha track dbSnp153Composite compositeTrack on shortLabel dbSNP 153 longLabel Short Genetic Variants from dbSNP release 153 type bed 3 group varRep visibility hide url https://www.ncbi.nlm.nih.gov/snp/$$ urlLabel dbSNP: subGroup1 view Views variants=Variants errs=Mapping_Errors +maxWindowCoverage 4000000 priority 1 pennantIcon Note green ../goldenPath/newsarch.html "dbSNP 155 is now available, and dbSNP 153 will be nested into the dbSNP archive soon." track dbSnp153ViewVariants view variants parent dbSnp153Composite shortLabel Variants visibility dense type bigDbSnp detailsTabUrls _dataOffset=/gbdb/hgFixed/dbSnp/dbSnp153Details.tab.gz freqSourceOrder 1000Genomes,GnomAD_exomes,TOPMED,ExAC,PAGE_STUDY,GnomAD,GoESP,Estonian,ALSPAC,TWINSUK,NorthernSweden,Vietnamese classFilterValues snv,mnv,ins,del,delins,identity classFilterType multipleListOr showCfg on ucscNotesFilterValues \ @@ -1759,44 +1760,44 @@ bigDataUrl /gbdb/$D/snp/dbSnp153BadCoords.bb type bigBed 4 color 100,100,100 priority 5 track dbSnp155Composite compositeTrack on shortLabel dbSNP 155 longLabel Short Genetic Variants from dbSNP release 155 type bed 3 group varRep visibility pack url https://www.ncbi.nlm.nih.gov/snp/$$ urlLabel dbSNP: subGroup1 view Views variants=Variants errs=Mapping_Errors +maxWindowCoverage 4000000 priority 0.8 pennantIcon New red ../goldenPath/newsarch.html#082222 "Released Aug. 22, 2022" track dbSnp155ViewVariants view variants parent dbSnp155Composite shortLabel Variants visibility dense type bigDbSnp detailsTabUrls _dataOffset=/gbdb/hgFixed/dbSnp/dbSnp155Details.tab.gz freqSourceOrder 1000Genomes,dbGaP_PopFreq,TOPMED,KOREAN,SGDP_PRJ,Qatari,NorthernSweden,Siberian,TWINSUK,TOMMO,ALSPAC,GENOME_DK,GnomAD,GoNL,Estonian,Vietnamese,Korea1K,HapMap,PRJEB36033,HGDP_Stanford,Daghestan,PAGE_STUDY,Chileans,MGP,PRJEB37584,GoESP,ExAC,GnomAD_exomes,FINRISK,PharmGKB,PRJEB37766 classFilterValues snv,mnv,ins,del,delins,identity classFilterType multipleListOr - showCfg on 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,\ freqIncomplete|Frequency reported with incomplete allele data,\ freqIsAmbiguous|Frequency reported for allele with IUPAC ambiguous base(s),\ freqNotMapped|Frequency reported on different assembly but not mapped by dbSNP,\ freqNotRefAlt|Reference genome allele is not major allele in at least one project,\ @@ -1830,30 +1831,31 @@ 1619|nc_transcript_variant,\ 2|genic_upstream_transcript_variant,\ 1986|upstream_transcript_variant,\ 2152|genic_downstream_transcript_variant,\ 1987|downstream_transcript_variant,\ 1627|intron_variant maxFuncImpactFilterType multipleListOr track dbSnp155Common parent dbSnp155ViewVariants on subGroups view=variants shortLabel Common dbSNP(155) longLabel Common (1000 Genomes Phase 3 MAF >= 1%) Short Genetic Variants from dbSNP Release 155 defaultGeneTracks knownGene bigDataUrl /gbdb/$D/snp/dbSnp155Common.bb + showCfg on priority 1 track dbSnp155ClinVar parent dbSnp155ViewVariants off subGroups view=variants shortLabel ClinVar dbSNP(155) longLabel Short Genetic Variants from dbSNP Release 155 Included in ClinVar defaultGeneTracks knownGene bigDataUrl /gbdb/$D/snp/dbSnp155ClinVar.bb priority 2 track dbSnp155Mult parent dbSnp155ViewVariants off subGroups view=variants shortLabel Mult. dbSNP(155)