e4696ced7edf4d0a2a995f203a751a3782cc2f16
lrnassar
  Fri May 29 15:00:59 2026 -0700
Add EVA SNP Release 9 — unified pipeline for native + GenArk contributed tracks. refs #37517

Adds the unified evaSnp9.py pipeline at src/hg/makeDb/scripts/evaSnp/evaSnp9.py
that builds both native UCSC db bigBeds and GenArk contributed bigBeds from
one driver, replacing the two separate v8 scripts (evaSnp8.py +
evaSnpGenArk.py). Built 40 native + 115 contributed tracks for v9.

trackDb: evaSnp9 subtrack added to the evaSnpContainer composite with the
new SNV/indel/MNV varClass labels, searchTable stanza, and
parent=on/visibility=dense defaults; evaSnp8 left on per QA preference.

evaSnpContainer.html: transition note explaining the v9 SO-label refresh
(SNV/deletion/insertion/indel/MNV/sequence_alteration replacing the legacy
substitution/delins/multipleNucleotideVariant labels in v3-v8) and the new
single-most-severe ucscClass convention; SO term list updated to dual-label
each entry; download example URL bumped to evaSnp9.bb.

Makedoc at src/hg/makeDb/doc/evaSnp9.txt documents the unified build,
deploy, and per-clade GenArk make steps.

diff --git src/hg/makeDb/trackDb/evaSnp.ra src/hg/makeDb/trackDb/evaSnp.ra
index c4bae15c13a..26a2a291414 100644
--- src/hg/makeDb/trackDb/evaSnp.ra
+++ src/hg/makeDb/trackDb/evaSnp.ra
@@ -142,15 +142,41 @@
 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 evaSnp8
 searchType bigBed
 searchMethod exact
 padding 2
+
+track evaSnp9
+shortLabel EVA SNP Release 9
+longLabel Short Genetic Variants from European Variant Archive Release 9
+type bigBed 9 +
+parent evaSnpContainer on
+visibility dense
+itemRgb on
+mouseOver <b>Ref/Alt allele(s)</b>: $ref>$alt<br> <b>Var type</b>: $ucscClass<br> <b>AA change</b>: $aaChange
+bigDataUrl /gbdb/$D/bbi/evaSnp9.bb
+url https://www.ebi.ac.uk/eva/?variant&accessionID=$$
+filterValues.varClass SNV|SNV,deletion|Deletion,insertion|Insertion,indel|Indel,MNV|MNV,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 evaSnp9
+searchType bigBed
+searchMethod exact
+padding 2