7039e0813fcb8d36a43b3b115b47781ea20488b4 angie Tue Mar 11 10:02:10 2025 -0700 Fix frameshift filter setting for dbSnp153 (SO term encoded as 865 not 0865) and dbSnp155 (different SO term: 1589 frameshift_variant instead of 865 frameshift). refs #35344 diff --git src/hg/makeDb/trackDb/human/trackDb.ra src/hg/makeDb/trackDb/human/trackDb.ra index b55982a05b1..4ddf1586c5a 100644 --- src/hg/makeDb/trackDb/human/trackDb.ra +++ src/hg/makeDb/trackDb/human/trackDb.ra @@ -1621,50 +1621,30 @@ 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 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 track dbSnp153ViewVariants @@ -1697,31 +1677,31 @@ 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 maxFuncImpactFilterLabel Greatest functional impact on gene maxFuncImpactFilterValues 0|(not annotated),\ - 0865|frameshift,\ + 865|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,\ @@ -1824,31 +1804,31 @@ 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 maxFuncImpactFilterLabel Greatest functional impact on gene maxFuncImpactFilterValues 0|(not annotated),\ - 0865|frameshift,\ + 1589|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,\ 2|genic_upstream_transcript_variant,\ 1986|upstream_transcript_variant,\ 2152|genic_downstream_transcript_variant,\ 1987|downstream_transcript_variant,\