482cc4cb3426acbc68d9410a92988729f0928c18 gperez2 Fri Dec 19 13:55:57 2025 -0800 Releasing the EVA Release 8 tracks, refs #36512 diff --git src/hg/makeDb/trackDb/evaSnp.ra src/hg/makeDb/trackDb/evaSnp.ra index 57571341f44..cf459044ccd 100644 --- src/hg/makeDb/trackDb/evaSnp.ra +++ src/hg/makeDb/trackDb/evaSnp.ra @@ -1,131 +1,158 @@ track evaSnpContainer shortLabel EVA SNP longLabel Short Genetic Variants from European Variant Archive group varRep type bigBed 9 + compositeTrack on visibility dense +pennantIcon Updated red ../goldenPath/newsarch.html#121925 "New EVA SNP Release 8 track Dec. 19, 2025" track evaSnp shortLabel EVA SNP Release 3 longLabel Short Genetic Variants from European Variant Archive Release 3 type bigBed 9 + parent evaSnpContainer off itemRgb on mouseOver Ref/Alt allele(s): $ref>$alt
Var type: $ucscClass
AA change: $aaChange bigDataUrl /gbdb/$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 + parent evaSnpContainer off visibility hide itemRgb on mouseOver Ref/Alt allele(s): $ref>$alt
Var type: $ucscClass
AA change: $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 + parent evaSnpContainer off itemRgb on mouseOver Ref/Alt allele(s): $ref>$alt
Var type: $ucscClass
AA change: $aaChange bigDataUrl /gbdb/$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 evaSnp6 shortLabel EVA SNP Release 6 longLabel Short Genetic Variants from European Variant Archive Release 6 type bigBed 9 + parent evaSnpContainer off itemRgb on mouseOver Ref/Alt allele(s): $ref>$alt
Var type: $ucscClass
AA change: $aaChange bigDataUrl /gbdb/$D/bbi/evaSnp6.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 html evaSnpContainer searchTable evaSnp6 searchType bigBed searchMethod exact padding 20 track evaSnp7 shortLabel EVA SNP Release 7 longLabel Short Genetic Variants from European Variant Archive Release 7 type bigBed 9 + -parent evaSnpContainer on -visibility dense +parent evaSnpContainer off itemRgb on mouseOver Ref/Alt allele(s): $ref>$alt
Var type: $ucscClass
AA change: $aaChange bigDataUrl /gbdb/$D/bbi/evaSnp7.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 html evaSnpContainer searchTable evaSnp7 searchType bigBed searchMethod exact padding 20 + +track evaSnp8 +shortLabel EVA SNP Release 8 +longLabel Short Genetic Variants from European Variant Archive Release 8 +type bigBed 9 + +parent evaSnpContainer on +visibility dense +itemRgb on +mouseOver Ref/Alt allele(s): $ref>$alt
Var type: $ucscClass
AA change: $aaChange +bigDataUrl /gbdb/$D/bbi/evaSnp8.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 +html evaSnpContainer +pennantIcon New red ../goldenPath/newsarch.html#121925 "Released Dec. 19, 2025" + +searchTable evaSnp8 +searchType bigBed +searchMethod exact +padding 2