711684a07793b68eabf1281c5a6cca8bd6fa2183 lrnassar Wed Jul 24 16:35:34 2024 -0700 Staging evaSnp6 track refs #34119 diff --git src/hg/makeDb/trackDb/trackDb.ra src/hg/makeDb/trackDb/trackDb.ra index b3a91ae..664792b 100644 --- src/hg/makeDb/trackDb/trackDb.ra +++ src/hg/makeDb/trackDb/trackDb.ra @@ -12,30 +12,32 @@ include trackDb.chainNet.fish.ra include trackDb.chainNet.insects.ra include trackDb.chainNet.other.ra include trackDb.chainNet.asmHub.ra include trackDb.encode3.ra include trackDb.transMap.ra include trackDb.nt.ra include trackDb.genbank.ra include uniprot.ra include jaspar.ra +include evaSnp.ra + # Root trackDb.ra file. Files from the organism subdirectory and the database sub-sub directory # will be layered on. Organism is something like 'human' and database is something # like 'hg18'. See the README file in this directory for a description of the format. # track stsMarker shortLabel STS Markers longLabel STS Markers on Genetic (blue), FISH (green) and RH (black) Maps group map visibility dense altColor 128,128,255, type bed 5 + track stsMap shortLabel STS Markers @@ -2996,105 +2998,30 @@ shortLabel Gap Overlaps longLabel Paired exactly identical sequence on each side of a gap track tandemDups parent tanDups on shortLabel Tandem Dups longLabel Paired exactly identical sequence survey over entire genome assembly track tantan shortLabel tantan Repeats longLabel Repeats by tantan group varRep visibility hide type bed 3 . -track evaSnp -shortLabel EVA SNP Release 3 -longLabel Short Genetic Variants from European Variant Archive Release 3 -type bigBed 9 + -group varRep -visibility hide -itemRgb on -mouseOver $ref>$alt $ucscClass $aaChange -bigDataUrl /gbdb/$D/bbi/evaSnp.bb -url https://www.ebi.ac.uk/eva/?variant&accessionID=$$ -filterValues.varClass deletion|Deletion,delins|Deletion-Insertion,insertion|Insertion,multipleNucleotideSubstitution|Multiple nucleotide substitution,substitution|Substitution,sequence alteration|Sequence alteration -filterLabel.varClass Variant class from EVA SO term -filterLabel.ucscClass Functional effect per UCSC Variant Annotation -filterValues.ucscClass downstream_gene_variant|Downstream gene variant,upstream_gene_variant|Upstream gene variant,intron_variant|Intron variant,NMD_transcript_variant|Nonsense-mediated mRNA decay (NMD) variant,5_prime_UTR_variant|5 prime UTR variant,3_prime_UTR_variant|3 prime UTR variant,missense_variant|Missense variant,synonymous_variant|Synonymous variant,non_coding_transcript_exon_variant|Non-coding transcript exon variant,no_sequence_alteration|No sequence alteration,splice_region_variant|Splice region variant,frameshift_variant|Frameshift variant,stop_gained|Stop gained,splice_acceptor_variant|Splice acceptor variant,inframe_deletion|Inframe deletion,inframe_insertion|Inframe insertion,splice_donor_variant|Splice donor variant,coding_sequence_variant|Coding sequence variant,initiator_codon_variant|Initiator codon variant,stop_lost|Stop lost,stop_retained_variant|Stop retained variant,intergenic_variant|Intergenic variant -filterType.ucscClass multipleListOnlyOr -filterValues.itemRgb 255,,0,,0|Protein-altering and splice variants,0,,128,,0|Synonymous variants,0,,0,,255|Non-coding transcripts or UTR variants,0,,0,,0|Intergenic and intronic variants -filterLabel.itemRgb General variant types by color grouping -maxWindowCoverage 250000 -maxItems 1000000 - -searchTable evaSnp -searchType bigBed -searchMethod exact -padding 20 - -track evaSnp4 -shortLabel EVA SNP Release 4 -longLabel Short Genetic Variants from European Variant Archive Release 4 -type bigBed 9 + -group varRep -visibility hide -itemRgb on -mouseOver $ref>$alt $ucscClass $aaChange -bigDataUrl /gbdb/$D/bbi/evaSnp4.bb -url https://www.ebi.ac.uk/eva/?variant&accessionID=$$ -filterValues.varClass deletion|Deletion,delins|Deletion-Insertion,insertion|Insertion,multipleNucleotideSubstitution|Multiple nucleotide substitution,substitution|Substitution,sequence alteration|Sequence alteration -filterLabel.varClass Variant class from EVA SO term -filterLabel.ucscClass Functional effect per UCSC Variant Annotation -filterValues.ucscClass downstream_gene_variant|Downstream gene variant,upstream_gene_variant|Upstream gene variant,intron_variant|Intron variant,NMD_transcript_variant|Nonsense-mediated mRNA decay (NMD) variant,5_prime_UTR_variant|5 prime UTR variant,3_prime_UTR_variant|3 prime UTR variant,missense_variant|Missense variant,synonymous_variant|Synonymous variant,non_coding_transcript_exon_variant|Non-coding transcript exon variant,no_sequence_alteration|No sequence alteration,splice_region_variant|Splice region variant,frameshift_variant|Frameshift variant,stop_gained|Stop gained,splice_acceptor_variant|Splice acceptor variant,inframe_deletion|Inframe deletion,inframe_insertion|Inframe insertion,splice_donor_variant|Splice donor variant,coding_sequence_variant|Coding sequence variant,initiator_codon_variant|Initiator codon variant,stop_lost|Stop lost,stop_retained_variant|Stop retained variant,intergenic_variant|Intergenic variant -filterType.ucscClass multipleListOnlyOr -filterValues.itemRgb 255,,0,,0|Protein-altering and splice variants,0,,128,,0|Synonymous variants,0,,0,,255|Non-coding transcripts or UTR variants,0,,0,,0|Intergenic and intronic variants -filterLabel.itemRgb General variant types by color grouping -maxWindowCoverage 250000 -maxItems 1000000 - -searchTable evaSnp4 -searchType bigBed -searchMethod exact -padding 20 - -track evaSnp5 -shortLabel EVA SNP Release 5 -longLabel Short Genetic Variants from European Variant Archive Release 5 -type bigBed 9 + -group varRep -visibility dense -itemRgb on -mouseOver $ref>$alt $ucscClass $aaChange -bigDataUrl /gbdb/$D/bbi/evaSnp5.bb -url https://www.ebi.ac.uk/eva/?variant&accessionID=$$ -filterValues.varClass deletion|Deletion,delins|Deletion-Insertion,insertion|Insertion,multipleNucleotideSubstitution|Multiple nucleotide substitution,substitution|Substitution,sequence alteration|Sequence alteration -filterLabel.varClass Variant class from EVA SO term -filterLabel.ucscClass Functional effect per UCSC Variant Annotation -filterValues.ucscClass downstream_gene_variant|Downstream gene variant,upstream_gene_variant|Upstream gene variant,intron_variant|Intron variant,NMD_transcript_variant|Nonsense-mediated mRNA decay (NMD) variant,5_prime_UTR_variant|5 prime UTR variant,3_prime_UTR_variant|3 prime UTR variant,missense_variant|Missense variant,synonymous_variant|Synonymous variant,non_coding_transcript_exon_variant|Non-coding transcript exon variant,no_sequence_alteration|No sequence alteration,splice_region_variant|Splice region variant,frameshift_variant|Frameshift variant,stop_gained|Stop gained,splice_acceptor_variant|Splice acceptor variant,inframe_deletion|Inframe deletion,inframe_insertion|Inframe insertion,splice_donor_variant|Splice donor variant,coding_sequence_variant|Coding sequence variant,initiator_codon_variant|Initiator codon variant,stop_lost|Stop lost,stop_retained_variant|Stop retained variant,intergenic_variant|Intergenic variant -filterType.ucscClass multipleListOnlyOr -filterValues.itemRgb 255,,0,,0|Protein-altering and splice variants,0,,128,,0|Synonymous variants,0,,0,,255|Non-coding transcripts or UTR variants,0,,0,,0|Intergenic and intronic variants -filterLabel.itemRgb General variant types by color grouping -maxWindowCoverage 250000 -maxItems 1000000 - -searchTable evaSnp5 -searchType bigBed -searchMethod exact -padding 20 - track HLTOGAannotvHg38v1 bigDataUrl /gbdb/$D/TOGAvHg38v1/HLTOGAannotVsHg38v1.bb shortLabel TOGA vs. hg38 longLabel TOGA annotations using human/hg38 as reference group genes visibility hide itemRgb on type bigBed 12 searchIndex name searchTrix /gbdb/$D/TOGAvHg38v1/HLTOGAannotVsHg38v1.ix html TOGAannotation # searchTable HLTOGAannotvsHg38v1BIG # searchType bigBed # searchMethod fuzzy