5239d7622b288c5d897ca855808844b16c183833 gperez2 Tue Jun 10 16:00:17 2025 -0700 Releasing and announcing the EVA Release 7, refs #35504 diff --git src/hg/makeDb/trackDb/evaSnp.alpha.ra src/hg/makeDb/trackDb/evaSnp.alpha.ra deleted file mode 100644 index 9e4782c7cde..00000000000 --- src/hg/makeDb/trackDb/evaSnp.alpha.ra +++ /dev/null @@ -1,132 +0,0 @@ -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#060625 "Updated June 6, 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 $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 + -parent evaSnpContainer off -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 + -parent evaSnpContainer off -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 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 $ucscClass $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 -itemRgb on -mouseOver $ref>$alt $ucscClass $aaChange -bigDataUrl /gbdb/$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