f674b74547b883a2054c4771533d753266e07c06 lrnassar Mon May 4 16:21:54 2026 -0700 QA pass on varFreqs supertrack: relabel HGDP+1kG and AllOfUs per-population fields to match data semantics, expose all 7 GenomeAsia populations in filter UI, normalize labels and capitalization, add Methods + References to description page, and flag GenomeAsia GRCh37 coordinate mismatch via dataVersion. refs #36642 trackDb (varFreqs.ra): - HGDP+1kG per-population AC/AF labels relabeled from "gnomAD HGDP+1kG <pop>" to "gnomAD v3.1.2 <pop> (full release)" since the values come from the full ~76k-genome gnomAD release, not the 4,094-genome HGDP+1kG cohort. - AllOfUs per-population AC/AF labels appended with "(local ancestry)" to clarify these are local-ancestry-stratified haplotype frequencies (Ioannidis lab pipeline), not the AllOfUs paper's global Rye categories. - Added 8 new filter entries for GenomeAsia OCE/AMR/AFR/WER (data has 7 population groups; trackUI previously exposed only 3). - shortLabel shortenings: alfaVcf, finngen, gasp, gaspIndel, kova, saudi, schema, colorsDbSnv, tishkoff180. - longLabel shortenings: ga4kSnv, colorsDbSnv, svatalogSnv, tishkoff180. - Capitalization fixes: SFARI Spark to SFARI SPARK, Japan ToMMO to Japan ToMMo, NHLBI TOPMED to NHLBI TOPMed. - dataVersion added on 6 subtracks that lacked it (gasp, gaspIndel, indigenomes, saudi, ga4kSnv, svatalogSnv); gasp/gaspIndel flagged "Pilot 2019 (GRCh37 - to be lifted)" for visibility of the open hg19 issue. - Default visibility flipped: non-summary subtracks now dense, summary varFreqsAll now pack. Container stays hide. Description page (varFreqs.html): - Added References section with 21 primary publications for the source cohorts. - Added "Notes on Specific Sub-tracks" explaining the HGDP+1kG cohort vs full-release distinction and the AllOfUs locAncFreq semantics. - Added Methods section describing per-subtrack and combined-track build pipelines, with links to the GitHub scripts directory and makedoc. - Encoded genome@soe.ucsc.edu with encodeEmail.pl. - Corrected "more than 1.2 billion variants" to "1.17 billion" (actual varFreqsAll.bb itemCount: 1,169,063,801). - Normalized body-text quotes to " entities. - AllOfUs and HGDP+1kG rows in the datasets table now flag the semantic distinction inline. Build config (scripts/varFreqs/populations.tsv): - Added 4 GenomeAsia rows (OCE, AMR, AFR, WER) so the next varFreqsAll bigBed rebuild will populate the new filter columns. - Fixed HGDP1kG nfe label "European" to "Non-Finnish European" to match the trackdb relabel. diff --git src/hg/makeDb/scripts/varFreqs/populations.tsv src/hg/makeDb/scripts/varFreqs/populations.tsv index 9de0495455d..86333218b55 100644 --- src/hg/makeDb/scripts/varFreqs/populations.tsv +++ src/hg/makeDb/scripts/varFreqs/populations.tsv @@ -1,28 +1,32 @@ # Population breakdown configuration for varFreqsAll combined track # db_key pop_key pop_name ac_field af_field # AllOfUs local ancestry populations AllOfUs AFR African AC_AFR AF_AFR AllOfUs AMR Indigenous American AC_AMR AF_AMR AllOfUs EAS East Asian AC_EAS AF_EAS AllOfUs EUR European AC_EUR AF_EUR AllOfUs OCE Oceanian AC_OCE AF_OCE AllOfUs SAS South Asian AC_SAS AF_SAS -# GenomeAsia populations +# GenomeAsia populations (7 groups in source VCF) GenomeAsia NEA Northeast Asian AC_NEA AF_NEA GenomeAsia SEA Southeast Asian AC_SEA AF_SEA GenomeAsia SAS South Asian AC_SAS AF_SAS +GenomeAsia OCE Oceanian AC_OCE AF_OCE +GenomeAsia AMR American AC_AMR AF_AMR +GenomeAsia AFR African AC_AFR AF_AFR +GenomeAsia WER Western European Ref AC_WER AF_WER # gnomAD HGDP+1kG continental groups HGDP1kG afr African gnomad_AC_afr gnomad_AF_afr HGDP1kG ami Amish gnomad_AC_ami gnomad_AF_ami HGDP1kG amr Latino gnomad_AC_amr gnomad_AF_amr HGDP1kG asj Ashkenazi Jewish gnomad_AC_asj gnomad_AF_asj HGDP1kG eas East Asian gnomad_AC_eas gnomad_AF_eas HGDP1kG fin Finnish gnomad_AC_fin gnomad_AF_fin HGDP1kG mid Middle Eastern gnomad_AC_mid gnomad_AF_mid -HGDP1kG nfe European gnomad_AC_nfe gnomad_AF_nfe +HGDP1kG nfe Non-Finnish European gnomad_AC_nfe gnomad_AF_nfe HGDP1kG oth Other gnomad_AC_oth gnomad_AF_oth HGDP1kG sas South Asian gnomad_AC_sas gnomad_AF_sas # GREGoR affected/unaffected breakdown GREGoR AFF Affected AC_AFFECTED . GREGoR UNA Unaffected AC_UNAFFECTED . GREGoR UNK Unknown AC_UNKNOWN .