fe96ff900173bd8c6f9b27200b9f70383349869c
lrnassar
  Mon Apr 28 13:26:46 2025 -0700
Staging EVA SNP 7 as QA-ready, refs #35504

diff --git src/hg/makeDb/trackDb/evaSnp.alpha.ra src/hg/makeDb/trackDb/evaSnp.alpha.ra
new file mode 100644
index 00000000000..7d9b246e985
--- /dev/null
+++ src/hg/makeDb/trackDb/evaSnp.alpha.ra
@@ -0,0 +1,131 @@
+track evaSnpContainer
+shortLabel EVA SNP
+longLabel Short Genetic Variants from European Variant Archive
+group varRep
+type bigBed 9 +
+compositeTrack on
+visibility dense
+
+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