d379fe71f9062a15c3d0fe78ff64dd62edf9816e dschmelt Thu Apr 1 15:18:59 2021 -0700 dbSnpArchive track commit, with version controlled data files for 3 assemblies, outlines in detail in refs #26719 diff --git src/hg/makeDb/trackDb/human/trackDb.ra src/hg/makeDb/trackDb/human/trackDb.ra index c7524a7..6c9fc8b 100644 --- src/hg/makeDb/trackDb/human/trackDb.ra +++ src/hg/makeDb/trackDb/human/trackDb.ra @@ -1585,50 +1585,50 @@ group varRep visibility hide url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$ urlLabel dbSNP: defaultGeneTracks knownGene maxWindowToDraw 10000000 type bed 6 + trackHandler snp125 chimpOrangMacOrthoTable snp151OrthoPt5Pa2Rm8 chimpDb panTro5 orangDb ponAbe2 macaqueDb rheMac8 hapmapPhase III codingAnnotations snp151CodingDbSnp, -track dbSnp152 -shortLabel All dbSNP (152) -longLabel Short Genetic Variants from dbSNP release 152 -bigDataUrl /gbdb/$D/snp/dbSnp152.bb -detailsTabUrls _dataOffset=/gbdb/hgFixed/dbSnp/dbSnp152Details.tab.gz -group varRep -visibility hide -url https://www.ncbi.nlm.nih.gov/snp/$$ -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 -release alpha +#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 hide +#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 +#release alpha track dbSnp153Composite compositeTrack on shortLabel dbSNP 153 longLabel Short Genetic Variants from dbSNP release 153 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 priority 0.8 track dbSnp153ViewVariants view variants