533cc89eb4febc78c9f8f104aed4523de06bf85b max Fri Jun 19 08:58:02 2026 -0700 varFreqs: fix numeric filter rendering and trim per-cohort filters #Preview2 week - bugs introduced now will need a build patch to fix The Affected/Background track config pages showed none of the AF/AC/AN filters. hgTrackUi only discovers a numeric filter from a filter.<field> (or <field>Filter) setting (FILTER_NUMBER_WILDCARD in bigBedFilter.h); the generated fragment had only filterByRange.<field>/filterLimits.<field> for those fields, so they were silently dropped. vcfToBigBed.py now emits filter.<field> (a full-range default, so nothing is filtered by default) plus filterLimits for every numeric filter. That made ~140 filters appear, which overwhelmed the config page, so the per-database and per-population AF/AC filters are emitted commented out (range_filter enabled=False) and can be re-enabled individually by removing the leading "# ". Only the global filters remain active: variant type, consequence, the affected/case and background AF/AC/AN summaries, the affected/case-cohort and background-source selectors, the in-affected flag, and the length filters. The per-cohort data columns are unchanged in the bigBed and still show on the details page. No bigBed rebuild needed; this is trackDb-only. refs #36642 diff --git src/hg/makeDb/trackDb/human/varFreqs.ra src/hg/makeDb/trackDb/human/varFreqs.ra index bd0aef5a8e1..f056f6c92b0 100644 --- src/hg/makeDb/trackDb/human/varFreqs.ra +++ src/hg/makeDb/trackDb/human/varFreqs.ra @@ -1,1098 +1,1654 @@ track varFreqs shortLabel SNV Frequencies longLabel SNV Frequencies from various cohorts or national projects group varRep type bed 12 visibility hide superTrack on pennantIcon New red ../goldenPath/newsarch.html#TBD "Released TBD" track varFreqsAffected shortLabel Disease cohorts longLabel SNV Frequencies: variants in ~130,000 affected or case individuals (autism, schizophrenia, rare disease cohorts) type bigBed 9 + parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/_affected/varFreqsAffected.bb tableBrowser off visibility pack itemRgb on maxWindowToDraw 5000000 priority 0.11 mouseOver <b>Var:</b> ${name}<br><b>AA change:</b> ${aaChange}<br><b>Var type:</b> ${varType}<br><b>Conseq:</b> ${consequence}<br><b>Affected AF:</b> ${affectedAF}<br><b>Affected AC/AN:</b> ${affectedAC} / ${affectedAN}<br><b>Affected cohorts:</b> ${affectedCohorts}<br><b>Background AF:</b> ${backgroundAF} filterValues.affectedCohorts SPARK|SFARI SPARK WES,SFARI_WGS|SFARI SPARK WGS,GREGoR|GREGoR,SCHEMA|SCHEMA,GA4K|GA4K PacBio LR filterType.affectedCohorts multipleListOr filterLabel.affectedCohorts Affected/case cohort filterValues.backgroundSources AllOfUs|AllOfUs,SPARK|SFARI SPARK WES,SFARI_WGS|SFARI SPARK WGS,GenomeAsia|GenomeAsia SNVs,GenomeAsiaIndel|GenomeAsia Indels,NPM|NPM Singapore,KOVA|KOVA Korea,ToMMo|ToMMo Japan,FinnGen|FinnGen Finland,Saudi|Saudi,SweGen|SweGen Sweden,TOPMed|TOPMed,ABraOM|ABraOM Brazil,ALFA|ALFA,MGRB|MGRB Australia,HRC|HRC,SGDP|SGDP,HGDP1kG|gnomAD HGDP+1kG,GREGoR|GREGoR,SCHEMA|SCHEMA,CoLoRSdb|CoLoRSdb PacBio LR,SVatalog|SVatalog 101 10XG SR,Tishkoff180|Tishkoff 180 African WGS,WBBC|WBBC China,ChinaMAP|China ChinaMAP,GenomeIndia|GenomeIndia 9.7k WGS,GoNL|GoNL Netherlands ~13x SR filterType.backgroundSources multipleListOr filterLabel.backgroundSources Background source (population or unaffected) # Variant type and consequence filters filterValues.varType SNV|SNV,INS|Insertion,DEL|Deletion,MNV|MNV filterLabel.varType Variant Type filterValues.consequence missense|Missense,synonymous|Synonymous,stop_gained|Stop Gained,frameshift|Frameshift,splice_donor|Splice Donor,splice_acceptor|Splice Acceptor,intron|Intron,3_prime_utr|3' UTR,5_prime_utr|5' UTR,non_coding|Non-coding,.|Intergenic,others|Other filterType.consequence multipleListOr filterLabel.consequence Consequence # Length filters filterByRange.refLen on filterLabel.refLen Reference Length filter.refLen 1:28037 filterLimits.refLen 1:28037 filterByRange.altLen on filterLabel.altLen Alternate Length filter.altLen 1:6294 filterLimits.altLen 1:6294 filterByRange.varLen on filterLabel.varLen Length Change filter.varLen -28036:6293 filterLimits.varLen -28036:6293 # Affected/case frequency summary filterByRange.affectedAF on filterLabel.affectedAF Affected/case AF (pooled) + filter.affectedAF 0:1 filterLimits.affectedAF 0:1 filterByRange.affectedAC on filterLabel.affectedAC Affected/case AC + filter.affectedAC 0:500000 + filterLimits.affectedAC 0:500000 filterByRange.affectedAN on filterLabel.affectedAN Affected/case AN (pool denominator) + filter.affectedAN 0:500000 + filterLimits.affectedAN 0:500000 # Background (population + unaffected) frequency summary filterByRange.backgroundAF on filterLabel.backgroundAF Background AF (pooled) + filter.backgroundAF 0:1 filterLimits.backgroundAF 0:1 filterByRange.backgroundAC on filterLabel.backgroundAC Background AC (population + unaffected) + filter.backgroundAC 0:5000000 + filterLimits.backgroundAC 0:5000000 filterByRange.backgroundAN on filterLabel.backgroundAN Background AN (pool denominator) + filter.backgroundAN 0:5000000 + filterLimits.backgroundAN 0:5000000 # Affected/case membership flag filterByRange.inAffected on filterLabel.inAffected Seen in an affected/case arm (1=yes, 0=no) filter.inAffected 0:1 filterLimits.inAffected 0:1 - # Per-database AF filters - filterByRange.AllOfUsAF on - filterLabel.AllOfUsAF AllOfUs AF - filterByRange.SPARKAF on - filterLabel.SPARKAF SFARI SPARK WES AF - filterByRange.SFARI_WGSAF on - filterLabel.SFARI_WGSAF SFARI SPARK WGS AF - filterByRange.GenomeAsiaAF on - filterLabel.GenomeAsiaAF GenomeAsia SNVs AF - filterByRange.GenomeAsiaIndelAF on - filterLabel.GenomeAsiaIndelAF GenomeAsia Indels AF - filterByRange.NPMAF on - filterLabel.NPMAF NPM Singapore AF - filterByRange.KOVAAF on - filterLabel.KOVAAF KOVA Korea AF - filterByRange.ToMMoAF on - filterLabel.ToMMoAF ToMMo Japan AF - filterByRange.FinnGenAF on - filterLabel.FinnGenAF FinnGen Finland AF - filterByRange.SaudiAF on - filterLabel.SaudiAF Saudi AF - filterByRange.SweGenAF on - filterLabel.SweGenAF SweGen Sweden AF - filterByRange.TOPMedAF on - filterLabel.TOPMedAF TOPMed AF - filterByRange.ABraOMAF on - filterLabel.ABraOMAF ABraOM Brazil AF - filterByRange.ALFAAF on - filterLabel.ALFAAF ALFA AF - filterByRange.MGRBAF on - filterLabel.MGRBAF MGRB Australia AF - filterByRange.HRCAF on - filterLabel.HRCAF HRC AF - filterByRange.SGDPAF on - filterLabel.SGDPAF SGDP AF - filterByRange.HGDP1kGAF on - filterLabel.HGDP1kGAF gnomAD HGDP+1kG AF - filterByRange.GREGoRAF on - filterLabel.GREGoRAF GREGoR AF - filterByRange.SCHEMAAF on - filterLabel.SCHEMAAF SCHEMA AF - filterByRange.GA4KAF on - filterLabel.GA4KAF GA4K PacBio LR AF - filterByRange.CoLoRSdbAF on - filterLabel.CoLoRSdbAF CoLoRSdb PacBio LR AF - filterByRange.SVatalogAF on - filterLabel.SVatalogAF SVatalog 101 10XG SR AF - filterByRange.Tishkoff180AF on - filterLabel.Tishkoff180AF Tishkoff 180 African WGS AF - filterByRange.WBBCAF on - filterLabel.WBBCAF WBBC China AF - filterByRange.ChinaMAPAF on - filterLabel.ChinaMAPAF China ChinaMAP AF - filterByRange.GenomeIndiaAF on - filterLabel.GenomeIndiaAF GenomeIndia 9.7k WGS AF - filterByRange.GoNLAF on - filterLabel.GoNLAF GoNL Netherlands ~13x SR AF - # Per-database AC filters - filterByRange.AllOfUsAC on - filterLabel.AllOfUsAC AllOfUs AC - filterByRange.SPARKAC on - filterLabel.SPARKAC SFARI SPARK WES AC - filterByRange.SFARI_WGSAC on - filterLabel.SFARI_WGSAC SFARI SPARK WGS AC - filterByRange.GenomeAsiaAC on - filterLabel.GenomeAsiaAC GenomeAsia SNVs AC - filterByRange.GenomeAsiaIndelAC on - filterLabel.GenomeAsiaIndelAC GenomeAsia Indels AC - filterByRange.NPMAC on - filterLabel.NPMAC NPM Singapore AC - filterByRange.KOVAAC on - filterLabel.KOVAAC KOVA Korea AC - filterByRange.ToMMoAC on - filterLabel.ToMMoAC ToMMo Japan AC - filterByRange.FinnGenAC on - filterLabel.FinnGenAC FinnGen Finland AC - filterByRange.SaudiAC on - filterLabel.SaudiAC Saudi AC - filterByRange.SweGenAC on - filterLabel.SweGenAC SweGen Sweden AC - filterByRange.TOPMedAC on - filterLabel.TOPMedAC TOPMed AC - filterByRange.ABraOMAC on - filterLabel.ABraOMAC ABraOM Brazil AC - filterByRange.ALFAAC on - filterLabel.ALFAAC ALFA AC - filterByRange.MGRBAC on - filterLabel.MGRBAC MGRB Australia AC - filterByRange.HRCAC on - filterLabel.HRCAC HRC AC - filterByRange.SGDPAC on - filterLabel.SGDPAC SGDP AC - filterByRange.HGDP1kGAC on - filterLabel.HGDP1kGAC gnomAD HGDP+1kG AC - filterByRange.GREGoRAC on - filterLabel.GREGoRAC GREGoR AC - filterByRange.SCHEMAAC on - filterLabel.SCHEMAAC SCHEMA AC - filterByRange.GA4KAC on - filterLabel.GA4KAC GA4K PacBio LR AC - filterByRange.CoLoRSdbAC on - filterLabel.CoLoRSdbAC CoLoRSdb PacBio LR AC - filterByRange.SVatalogAC on - filterLabel.SVatalogAC SVatalog 101 10XG SR AC - filterByRange.Tishkoff180AC on - filterLabel.Tishkoff180AC Tishkoff 180 African WGS AC - filterByRange.WBBCAC on - filterLabel.WBBCAC WBBC China AC - filterByRange.ChinaMAPAC on - filterLabel.ChinaMAPAC China ChinaMAP AC - filterByRange.GenomeIndiaAC on - filterLabel.GenomeIndiaAC GenomeIndia 9.7k WGS AC - filterByRange.GoNLAC on - filterLabel.GoNLAC GoNL Netherlands ~13x SR AC - # Population-specific AF filters + # Per-database AF filters (commented out: re-enable as needed) + # filterByRange.AllOfUsAF on + # filterLabel.AllOfUsAF AllOfUs AF + # filter.AllOfUsAF 0:1 + # filterLimits.AllOfUsAF 0:1 + # filterByRange.SPARKAF on + # filterLabel.SPARKAF SFARI SPARK WES AF + # filter.SPARKAF 0:1 + # filterLimits.SPARKAF 0:1 + # filterByRange.SFARI_WGSAF on + # filterLabel.SFARI_WGSAF SFARI SPARK WGS AF + # filter.SFARI_WGSAF 0:1 + # filterLimits.SFARI_WGSAF 0:1 + # filterByRange.GenomeAsiaAF on + # filterLabel.GenomeAsiaAF GenomeAsia SNVs AF + # filter.GenomeAsiaAF 0:1 + # filterLimits.GenomeAsiaAF 0:1 + # filterByRange.GenomeAsiaIndelAF on + # filterLabel.GenomeAsiaIndelAF GenomeAsia Indels AF + # filter.GenomeAsiaIndelAF 0:1 + # filterLimits.GenomeAsiaIndelAF 0:1 + # filterByRange.NPMAF on + # filterLabel.NPMAF NPM Singapore AF + # filter.NPMAF 0:1 + # filterLimits.NPMAF 0:1 + # filterByRange.KOVAAF on + # filterLabel.KOVAAF KOVA Korea AF + # filter.KOVAAF 0:1 + # filterLimits.KOVAAF 0:1 + # filterByRange.ToMMoAF on + # filterLabel.ToMMoAF ToMMo Japan AF + # filter.ToMMoAF 0:1 + # filterLimits.ToMMoAF 0:1 + # filterByRange.FinnGenAF on + # filterLabel.FinnGenAF FinnGen Finland AF + # filter.FinnGenAF 0:1 + # filterLimits.FinnGenAF 0:1 + # filterByRange.SaudiAF on + # filterLabel.SaudiAF Saudi AF + # filter.SaudiAF 0:1 + # filterLimits.SaudiAF 0:1 + # filterByRange.SweGenAF on + # filterLabel.SweGenAF SweGen Sweden AF + # filter.SweGenAF 0:1 + # filterLimits.SweGenAF 0:1 + # filterByRange.TOPMedAF on + # filterLabel.TOPMedAF TOPMed AF + # filter.TOPMedAF 0:1 + # filterLimits.TOPMedAF 0:1 + # filterByRange.ABraOMAF on + # filterLabel.ABraOMAF ABraOM Brazil AF + # filter.ABraOMAF 0:1 + # filterLimits.ABraOMAF 0:1 + # filterByRange.ALFAAF on + # filterLabel.ALFAAF ALFA AF + # filter.ALFAAF 0:1 + # filterLimits.ALFAAF 0:1 + # filterByRange.MGRBAF on + # filterLabel.MGRBAF MGRB Australia AF + # filter.MGRBAF 0:1 + # filterLimits.MGRBAF 0:1 + # filterByRange.HRCAF on + # filterLabel.HRCAF HRC AF + # filter.HRCAF 0:1 + # filterLimits.HRCAF 0:1 + # filterByRange.SGDPAF on + # filterLabel.SGDPAF SGDP AF + # filter.SGDPAF 0:1 + # filterLimits.SGDPAF 0:1 + # filterByRange.HGDP1kGAF on + # filterLabel.HGDP1kGAF gnomAD HGDP+1kG AF + # filter.HGDP1kGAF 0:1 + # filterLimits.HGDP1kGAF 0:1 + # filterByRange.GREGoRAF on + # filterLabel.GREGoRAF GREGoR AF + # filter.GREGoRAF 0:1 + # filterLimits.GREGoRAF 0:1 + # filterByRange.SCHEMAAF on + # filterLabel.SCHEMAAF SCHEMA AF + # filter.SCHEMAAF 0:1 + # filterLimits.SCHEMAAF 0:1 + # filterByRange.GA4KAF on + # filterLabel.GA4KAF GA4K PacBio LR AF + # filter.GA4KAF 0:1 + # filterLimits.GA4KAF 0:1 + # filterByRange.CoLoRSdbAF on + # filterLabel.CoLoRSdbAF CoLoRSdb PacBio LR AF + # filter.CoLoRSdbAF 0:1 + # filterLimits.CoLoRSdbAF 0:1 + # filterByRange.SVatalogAF on + # filterLabel.SVatalogAF SVatalog 101 10XG SR AF + # filter.SVatalogAF 0:1 + # filterLimits.SVatalogAF 0:1 + # filterByRange.Tishkoff180AF on + # filterLabel.Tishkoff180AF Tishkoff 180 African WGS AF + # filter.Tishkoff180AF 0:1 + # filterLimits.Tishkoff180AF 0:1 + # filterByRange.WBBCAF on + # filterLabel.WBBCAF WBBC China AF + # filter.WBBCAF 0:1 + # filterLimits.WBBCAF 0:1 + # filterByRange.ChinaMAPAF on + # filterLabel.ChinaMAPAF China ChinaMAP AF + # filter.ChinaMAPAF 0:1 + # filterLimits.ChinaMAPAF 0:1 + # filterByRange.GenomeIndiaAF on + # filterLabel.GenomeIndiaAF GenomeIndia 9.7k WGS AF + # filter.GenomeIndiaAF 0:1 + # filterLimits.GenomeIndiaAF 0:1 + # filterByRange.GoNLAF on + # filterLabel.GoNLAF GoNL Netherlands ~13x SR AF + # filter.GoNLAF 0:1 + # filterLimits.GoNLAF 0:1 + # Per-database AC filters (commented out: re-enable as needed) + # filterByRange.AllOfUsAC on + # filterLabel.AllOfUsAC AllOfUs AC + # filter.AllOfUsAC 0:2000000 + # filterLimits.AllOfUsAC 0:2000000 + # filterByRange.SPARKAC on + # filterLabel.SPARKAC SFARI SPARK WES AC + # filter.SPARKAC 0:2000000 + # filterLimits.SPARKAC 0:2000000 + # filterByRange.SFARI_WGSAC on + # filterLabel.SFARI_WGSAC SFARI SPARK WGS AC + # filter.SFARI_WGSAC 0:2000000 + # filterLimits.SFARI_WGSAC 0:2000000 + # filterByRange.GenomeAsiaAC on + # filterLabel.GenomeAsiaAC GenomeAsia SNVs AC + # filter.GenomeAsiaAC 0:2000000 + # filterLimits.GenomeAsiaAC 0:2000000 + # filterByRange.GenomeAsiaIndelAC on + # filterLabel.GenomeAsiaIndelAC GenomeAsia Indels AC + # filter.GenomeAsiaIndelAC 0:2000000 + # filterLimits.GenomeAsiaIndelAC 0:2000000 + # filterByRange.NPMAC on + # filterLabel.NPMAC NPM Singapore AC + # filter.NPMAC 0:2000000 + # filterLimits.NPMAC 0:2000000 + # filterByRange.KOVAAC on + # filterLabel.KOVAAC KOVA Korea AC + # filter.KOVAAC 0:2000000 + # filterLimits.KOVAAC 0:2000000 + # filterByRange.ToMMoAC on + # filterLabel.ToMMoAC ToMMo Japan AC + # filter.ToMMoAC 0:2000000 + # filterLimits.ToMMoAC 0:2000000 + # filterByRange.FinnGenAC on + # filterLabel.FinnGenAC FinnGen Finland AC + # filter.FinnGenAC 0:2000000 + # filterLimits.FinnGenAC 0:2000000 + # filterByRange.SaudiAC on + # filterLabel.SaudiAC Saudi AC + # filter.SaudiAC 0:2000000 + # filterLimits.SaudiAC 0:2000000 + # filterByRange.SweGenAC on + # filterLabel.SweGenAC SweGen Sweden AC + # filter.SweGenAC 0:2000000 + # filterLimits.SweGenAC 0:2000000 + # filterByRange.TOPMedAC on + # filterLabel.TOPMedAC TOPMed AC + # filter.TOPMedAC 0:2000000 + # filterLimits.TOPMedAC 0:2000000 + # filterByRange.ABraOMAC on + # filterLabel.ABraOMAC ABraOM Brazil AC + # filter.ABraOMAC 0:2000000 + # filterLimits.ABraOMAC 0:2000000 + # filterByRange.ALFAAC on + # filterLabel.ALFAAC ALFA AC + # filter.ALFAAC 0:2000000 + # filterLimits.ALFAAC 0:2000000 + # filterByRange.MGRBAC on + # filterLabel.MGRBAC MGRB Australia AC + # filter.MGRBAC 0:2000000 + # filterLimits.MGRBAC 0:2000000 + # filterByRange.HRCAC on + # filterLabel.HRCAC HRC AC + # filter.HRCAC 0:2000000 + # filterLimits.HRCAC 0:2000000 + # filterByRange.SGDPAC on + # filterLabel.SGDPAC SGDP AC + # filter.SGDPAC 0:2000000 + # filterLimits.SGDPAC 0:2000000 + # filterByRange.HGDP1kGAC on + # filterLabel.HGDP1kGAC gnomAD HGDP+1kG AC + # filter.HGDP1kGAC 0:2000000 + # filterLimits.HGDP1kGAC 0:2000000 + # filterByRange.GREGoRAC on + # filterLabel.GREGoRAC GREGoR AC + # filter.GREGoRAC 0:2000000 + # filterLimits.GREGoRAC 0:2000000 + # filterByRange.SCHEMAAC on + # filterLabel.SCHEMAAC SCHEMA AC + # filter.SCHEMAAC 0:2000000 + # filterLimits.SCHEMAAC 0:2000000 + # filterByRange.GA4KAC on + # filterLabel.GA4KAC GA4K PacBio LR AC + # filter.GA4KAC 0:2000000 + # filterLimits.GA4KAC 0:2000000 + # filterByRange.CoLoRSdbAC on + # filterLabel.CoLoRSdbAC CoLoRSdb PacBio LR AC + # filter.CoLoRSdbAC 0:2000000 + # filterLimits.CoLoRSdbAC 0:2000000 + # filterByRange.SVatalogAC on + # filterLabel.SVatalogAC SVatalog 101 10XG SR AC + # filter.SVatalogAC 0:2000000 + # filterLimits.SVatalogAC 0:2000000 + # filterByRange.Tishkoff180AC on + # filterLabel.Tishkoff180AC Tishkoff 180 African WGS AC + # filter.Tishkoff180AC 0:2000000 + # filterLimits.Tishkoff180AC 0:2000000 + # filterByRange.WBBCAC on + # filterLabel.WBBCAC WBBC China AC + # filter.WBBCAC 0:2000000 + # filterLimits.WBBCAC 0:2000000 + # filterByRange.ChinaMAPAC on + # filterLabel.ChinaMAPAC China ChinaMAP AC + # filter.ChinaMAPAC 0:2000000 + # filterLimits.ChinaMAPAC 0:2000000 + # filterByRange.GenomeIndiaAC on + # filterLabel.GenomeIndiaAC GenomeIndia 9.7k WGS AC + # filter.GenomeIndiaAC 0:2000000 + # filterLimits.GenomeIndiaAC 0:2000000 + # filterByRange.GoNLAC on + # filterLabel.GoNLAC GoNL Netherlands ~13x SR AC + # filter.GoNLAC 0:2000000 + # filterLimits.GoNLAC 0:2000000 + # Population-specific AF/AC filters (commented out: re-enable as needed) # AllOfUs populations - filterByRange.AllOfUsAF_AFR on - filterLabel.AllOfUsAF_AFR AllOfUs African AF - filterByRange.AllOfUsAF_AMR on - filterLabel.AllOfUsAF_AMR AllOfUs Indigenous American AF - filterByRange.AllOfUsAF_EAS on - filterLabel.AllOfUsAF_EAS AllOfUs East Asian AF - filterByRange.AllOfUsAF_EUR on - filterLabel.AllOfUsAF_EUR AllOfUs European AF - filterByRange.AllOfUsAF_OCE on - filterLabel.AllOfUsAF_OCE AllOfUs Oceanian AF - filterByRange.AllOfUsAF_SAS on - filterLabel.AllOfUsAF_SAS AllOfUs South Asian AF - filterByRange.AllOfUsAC_AFR on - filterLabel.AllOfUsAC_AFR AllOfUs African AC - filterByRange.AllOfUsAC_AMR on - filterLabel.AllOfUsAC_AMR AllOfUs Indigenous American AC - filterByRange.AllOfUsAC_EAS on - filterLabel.AllOfUsAC_EAS AllOfUs East Asian AC - filterByRange.AllOfUsAC_EUR on - filterLabel.AllOfUsAC_EUR AllOfUs European AC - filterByRange.AllOfUsAC_OCE on - filterLabel.AllOfUsAC_OCE AllOfUs Oceanian AC - filterByRange.AllOfUsAC_SAS on - filterLabel.AllOfUsAC_SAS AllOfUs South Asian AC + # filterByRange.AllOfUsAF_AFR on + # filterLabel.AllOfUsAF_AFR AllOfUs African AF + # filter.AllOfUsAF_AFR 0:1 + # filterLimits.AllOfUsAF_AFR 0:1 + # filterByRange.AllOfUsAF_AMR on + # filterLabel.AllOfUsAF_AMR AllOfUs Indigenous American AF + # filter.AllOfUsAF_AMR 0:1 + # filterLimits.AllOfUsAF_AMR 0:1 + # filterByRange.AllOfUsAF_EAS on + # filterLabel.AllOfUsAF_EAS AllOfUs East Asian AF + # filter.AllOfUsAF_EAS 0:1 + # filterLimits.AllOfUsAF_EAS 0:1 + # filterByRange.AllOfUsAF_EUR on + # filterLabel.AllOfUsAF_EUR AllOfUs European AF + # filter.AllOfUsAF_EUR 0:1 + # filterLimits.AllOfUsAF_EUR 0:1 + # filterByRange.AllOfUsAF_OCE on + # filterLabel.AllOfUsAF_OCE AllOfUs Oceanian AF + # filter.AllOfUsAF_OCE 0:1 + # filterLimits.AllOfUsAF_OCE 0:1 + # filterByRange.AllOfUsAF_SAS on + # filterLabel.AllOfUsAF_SAS AllOfUs South Asian AF + # filter.AllOfUsAF_SAS 0:1 + # filterLimits.AllOfUsAF_SAS 0:1 + # filterByRange.AllOfUsAC_AFR on + # filterLabel.AllOfUsAC_AFR AllOfUs African AC + # filter.AllOfUsAC_AFR 0:2000000 + # filterLimits.AllOfUsAC_AFR 0:2000000 + # filterByRange.AllOfUsAC_AMR on + # filterLabel.AllOfUsAC_AMR AllOfUs Indigenous American AC + # filter.AllOfUsAC_AMR 0:2000000 + # filterLimits.AllOfUsAC_AMR 0:2000000 + # filterByRange.AllOfUsAC_EAS on + # filterLabel.AllOfUsAC_EAS AllOfUs East Asian AC + # filter.AllOfUsAC_EAS 0:2000000 + # filterLimits.AllOfUsAC_EAS 0:2000000 + # filterByRange.AllOfUsAC_EUR on + # filterLabel.AllOfUsAC_EUR AllOfUs European AC + # filter.AllOfUsAC_EUR 0:2000000 + # filterLimits.AllOfUsAC_EUR 0:2000000 + # filterByRange.AllOfUsAC_OCE on + # filterLabel.AllOfUsAC_OCE AllOfUs Oceanian AC + # filter.AllOfUsAC_OCE 0:2000000 + # filterLimits.AllOfUsAC_OCE 0:2000000 + # filterByRange.AllOfUsAC_SAS on + # filterLabel.AllOfUsAC_SAS AllOfUs South Asian AC + # filter.AllOfUsAC_SAS 0:2000000 + # filterLimits.AllOfUsAC_SAS 0:2000000 # SFARI SPARK WES populations - filterByRange.SPARKAF_AUT on - filterLabel.SPARKAF_AUT SFARI SPARK WES ASD proband AF - filterByRange.SPARKAF_NON_AUT on - filterLabel.SPARKAF_NON_AUT SFARI SPARK WES Non-ASD family AF - filterByRange.SPARKAC_AUT on - filterLabel.SPARKAC_AUT SFARI SPARK WES ASD proband AC - filterByRange.SPARKAC_NON_AUT on - filterLabel.SPARKAC_NON_AUT SFARI SPARK WES Non-ASD family AC + # filterByRange.SPARKAF_AUT on + # filterLabel.SPARKAF_AUT SFARI SPARK WES ASD proband AF + # filter.SPARKAF_AUT 0:1 + # filterLimits.SPARKAF_AUT 0:1 + # filterByRange.SPARKAF_NON_AUT on + # filterLabel.SPARKAF_NON_AUT SFARI SPARK WES Non-ASD family AF + # filter.SPARKAF_NON_AUT 0:1 + # filterLimits.SPARKAF_NON_AUT 0:1 + # filterByRange.SPARKAC_AUT on + # filterLabel.SPARKAC_AUT SFARI SPARK WES ASD proband AC + # filter.SPARKAC_AUT 0:2000000 + # filterLimits.SPARKAC_AUT 0:2000000 + # filterByRange.SPARKAC_NON_AUT on + # filterLabel.SPARKAC_NON_AUT SFARI SPARK WES Non-ASD family AC + # filter.SPARKAC_NON_AUT 0:2000000 + # filterLimits.SPARKAC_NON_AUT 0:2000000 # SFARI SPARK WGS populations - filterByRange.SFARI_WGSAF_AUT on - filterLabel.SFARI_WGSAF_AUT SFARI SPARK WGS ASD proband AF - filterByRange.SFARI_WGSAF_NON_AUT on - filterLabel.SFARI_WGSAF_NON_AUT SFARI SPARK WGS Non-ASD family AF - filterByRange.SFARI_WGSAC_AUT on - filterLabel.SFARI_WGSAC_AUT SFARI SPARK WGS ASD proband AC - filterByRange.SFARI_WGSAC_NON_AUT on - filterLabel.SFARI_WGSAC_NON_AUT SFARI SPARK WGS Non-ASD family AC + # filterByRange.SFARI_WGSAF_AUT on + # filterLabel.SFARI_WGSAF_AUT SFARI SPARK WGS ASD proband AF + # filter.SFARI_WGSAF_AUT 0:1 + # filterLimits.SFARI_WGSAF_AUT 0:1 + # filterByRange.SFARI_WGSAF_NON_AUT on + # filterLabel.SFARI_WGSAF_NON_AUT SFARI SPARK WGS Non-ASD family AF + # filter.SFARI_WGSAF_NON_AUT 0:1 + # filterLimits.SFARI_WGSAF_NON_AUT 0:1 + # filterByRange.SFARI_WGSAC_AUT on + # filterLabel.SFARI_WGSAC_AUT SFARI SPARK WGS ASD proband AC + # filter.SFARI_WGSAC_AUT 0:2000000 + # filterLimits.SFARI_WGSAC_AUT 0:2000000 + # filterByRange.SFARI_WGSAC_NON_AUT on + # filterLabel.SFARI_WGSAC_NON_AUT SFARI SPARK WGS Non-ASD family AC + # filter.SFARI_WGSAC_NON_AUT 0:2000000 + # filterLimits.SFARI_WGSAC_NON_AUT 0:2000000 # GenomeAsia SNVs populations - filterByRange.GenomeAsiaAF_NEA on - filterLabel.GenomeAsiaAF_NEA GenomeAsia SNVs Northeast Asian AF - filterByRange.GenomeAsiaAF_SEA on - filterLabel.GenomeAsiaAF_SEA GenomeAsia SNVs Southeast Asian AF - filterByRange.GenomeAsiaAF_SAS on - filterLabel.GenomeAsiaAF_SAS GenomeAsia SNVs South Asian AF - filterByRange.GenomeAsiaAF_OCE on - filterLabel.GenomeAsiaAF_OCE GenomeAsia SNVs Oceanian AF - filterByRange.GenomeAsiaAF_AMR on - filterLabel.GenomeAsiaAF_AMR GenomeAsia SNVs American AF - filterByRange.GenomeAsiaAF_AFR on - filterLabel.GenomeAsiaAF_AFR GenomeAsia SNVs African AF - filterByRange.GenomeAsiaAF_WER on - filterLabel.GenomeAsiaAF_WER GenomeAsia SNVs Western European Ref AF - filterByRange.GenomeAsiaAC_NEA on - filterLabel.GenomeAsiaAC_NEA GenomeAsia SNVs Northeast Asian AC - filterByRange.GenomeAsiaAC_SEA on - filterLabel.GenomeAsiaAC_SEA GenomeAsia SNVs Southeast Asian AC - filterByRange.GenomeAsiaAC_SAS on - filterLabel.GenomeAsiaAC_SAS GenomeAsia SNVs South Asian AC - filterByRange.GenomeAsiaAC_OCE on - filterLabel.GenomeAsiaAC_OCE GenomeAsia SNVs Oceanian AC - filterByRange.GenomeAsiaAC_AMR on - filterLabel.GenomeAsiaAC_AMR GenomeAsia SNVs American AC - filterByRange.GenomeAsiaAC_AFR on - filterLabel.GenomeAsiaAC_AFR GenomeAsia SNVs African AC - filterByRange.GenomeAsiaAC_WER on - filterLabel.GenomeAsiaAC_WER GenomeAsia SNVs Western European Ref AC + # filterByRange.GenomeAsiaAF_NEA on + # filterLabel.GenomeAsiaAF_NEA GenomeAsia SNVs Northeast Asian AF + # filter.GenomeAsiaAF_NEA 0:1 + # filterLimits.GenomeAsiaAF_NEA 0:1 + # filterByRange.GenomeAsiaAF_SEA on + # filterLabel.GenomeAsiaAF_SEA GenomeAsia SNVs Southeast Asian AF + # filter.GenomeAsiaAF_SEA 0:1 + # filterLimits.GenomeAsiaAF_SEA 0:1 + # filterByRange.GenomeAsiaAF_SAS on + # filterLabel.GenomeAsiaAF_SAS GenomeAsia SNVs South Asian AF + # filter.GenomeAsiaAF_SAS 0:1 + # filterLimits.GenomeAsiaAF_SAS 0:1 + # filterByRange.GenomeAsiaAF_OCE on + # filterLabel.GenomeAsiaAF_OCE GenomeAsia SNVs Oceanian AF + # filter.GenomeAsiaAF_OCE 0:1 + # filterLimits.GenomeAsiaAF_OCE 0:1 + # filterByRange.GenomeAsiaAF_AMR on + # filterLabel.GenomeAsiaAF_AMR GenomeAsia SNVs American AF + # filter.GenomeAsiaAF_AMR 0:1 + # filterLimits.GenomeAsiaAF_AMR 0:1 + # filterByRange.GenomeAsiaAF_AFR on + # filterLabel.GenomeAsiaAF_AFR GenomeAsia SNVs African AF + # filter.GenomeAsiaAF_AFR 0:1 + # filterLimits.GenomeAsiaAF_AFR 0:1 + # filterByRange.GenomeAsiaAF_WER on + # filterLabel.GenomeAsiaAF_WER GenomeAsia SNVs Western European Ref AF + # filter.GenomeAsiaAF_WER 0:1 + # filterLimits.GenomeAsiaAF_WER 0:1 + # filterByRange.GenomeAsiaAC_NEA on + # filterLabel.GenomeAsiaAC_NEA GenomeAsia SNVs Northeast Asian AC + # filter.GenomeAsiaAC_NEA 0:2000000 + # filterLimits.GenomeAsiaAC_NEA 0:2000000 + # filterByRange.GenomeAsiaAC_SEA on + # filterLabel.GenomeAsiaAC_SEA GenomeAsia SNVs Southeast Asian AC + # filter.GenomeAsiaAC_SEA 0:2000000 + # filterLimits.GenomeAsiaAC_SEA 0:2000000 + # filterByRange.GenomeAsiaAC_SAS on + # filterLabel.GenomeAsiaAC_SAS GenomeAsia SNVs South Asian AC + # filter.GenomeAsiaAC_SAS 0:2000000 + # filterLimits.GenomeAsiaAC_SAS 0:2000000 + # filterByRange.GenomeAsiaAC_OCE on + # filterLabel.GenomeAsiaAC_OCE GenomeAsia SNVs Oceanian AC + # filter.GenomeAsiaAC_OCE 0:2000000 + # filterLimits.GenomeAsiaAC_OCE 0:2000000 + # filterByRange.GenomeAsiaAC_AMR on + # filterLabel.GenomeAsiaAC_AMR GenomeAsia SNVs American AC + # filter.GenomeAsiaAC_AMR 0:2000000 + # filterLimits.GenomeAsiaAC_AMR 0:2000000 + # filterByRange.GenomeAsiaAC_AFR on + # filterLabel.GenomeAsiaAC_AFR GenomeAsia SNVs African AC + # filter.GenomeAsiaAC_AFR 0:2000000 + # filterLimits.GenomeAsiaAC_AFR 0:2000000 + # filterByRange.GenomeAsiaAC_WER on + # filterLabel.GenomeAsiaAC_WER GenomeAsia SNVs Western European Ref AC + # filter.GenomeAsiaAC_WER 0:2000000 + # filterLimits.GenomeAsiaAC_WER 0:2000000 # NPM Singapore populations - filterByRange.NPMAF_Chinese on - filterLabel.NPMAF_Chinese NPM Singapore Singapore Chinese AF - filterByRange.NPMAF_Malay on - filterLabel.NPMAF_Malay NPM Singapore Singapore Malay AF - filterByRange.NPMAF_Indian on - filterLabel.NPMAF_Indian NPM Singapore Singapore Indian AF - filterByRange.NPMAC_Chinese on - filterLabel.NPMAC_Chinese NPM Singapore Singapore Chinese AC - filterByRange.NPMAC_Malay on - filterLabel.NPMAC_Malay NPM Singapore Singapore Malay AC - filterByRange.NPMAC_Indian on - filterLabel.NPMAC_Indian NPM Singapore Singapore Indian AC + # filterByRange.NPMAF_Chinese on + # filterLabel.NPMAF_Chinese NPM Singapore Singapore Chinese AF + # filter.NPMAF_Chinese 0:1 + # filterLimits.NPMAF_Chinese 0:1 + # filterByRange.NPMAF_Malay on + # filterLabel.NPMAF_Malay NPM Singapore Singapore Malay AF + # filter.NPMAF_Malay 0:1 + # filterLimits.NPMAF_Malay 0:1 + # filterByRange.NPMAF_Indian on + # filterLabel.NPMAF_Indian NPM Singapore Singapore Indian AF + # filter.NPMAF_Indian 0:1 + # filterLimits.NPMAF_Indian 0:1 + # filterByRange.NPMAC_Chinese on + # filterLabel.NPMAC_Chinese NPM Singapore Singapore Chinese AC + # filter.NPMAC_Chinese 0:2000000 + # filterLimits.NPMAC_Chinese 0:2000000 + # filterByRange.NPMAC_Malay on + # filterLabel.NPMAC_Malay NPM Singapore Singapore Malay AC + # filter.NPMAC_Malay 0:2000000 + # filterLimits.NPMAC_Malay 0:2000000 + # filterByRange.NPMAC_Indian on + # filterLabel.NPMAC_Indian NPM Singapore Singapore Indian AC + # filter.NPMAC_Indian 0:2000000 + # filterLimits.NPMAC_Indian 0:2000000 # gnomAD HGDP+1kG populations - filterByRange.HGDP1kGAF_afr on - filterLabel.HGDP1kGAF_afr gnomAD HGDP+1kG African AF - filterByRange.HGDP1kGAF_ami on - filterLabel.HGDP1kGAF_ami gnomAD HGDP+1kG Amish AF - filterByRange.HGDP1kGAF_amr on - filterLabel.HGDP1kGAF_amr gnomAD HGDP+1kG Latino AF - filterByRange.HGDP1kGAF_asj on - filterLabel.HGDP1kGAF_asj gnomAD HGDP+1kG Ashkenazi Jewish AF - filterByRange.HGDP1kGAF_eas on - filterLabel.HGDP1kGAF_eas gnomAD HGDP+1kG East Asian AF - filterByRange.HGDP1kGAF_fin on - filterLabel.HGDP1kGAF_fin gnomAD HGDP+1kG Finnish AF - filterByRange.HGDP1kGAF_mid on - filterLabel.HGDP1kGAF_mid gnomAD HGDP+1kG Middle Eastern AF - filterByRange.HGDP1kGAF_nfe on - filterLabel.HGDP1kGAF_nfe gnomAD HGDP+1kG Non-Finnish European AF - filterByRange.HGDP1kGAF_oth on - filterLabel.HGDP1kGAF_oth gnomAD HGDP+1kG Other AF - filterByRange.HGDP1kGAF_sas on - filterLabel.HGDP1kGAF_sas gnomAD HGDP+1kG South Asian AF - filterByRange.HGDP1kGAC_afr on - filterLabel.HGDP1kGAC_afr gnomAD HGDP+1kG African AC - filterByRange.HGDP1kGAC_ami on - filterLabel.HGDP1kGAC_ami gnomAD HGDP+1kG Amish AC - filterByRange.HGDP1kGAC_amr on - filterLabel.HGDP1kGAC_amr gnomAD HGDP+1kG Latino AC - filterByRange.HGDP1kGAC_asj on - filterLabel.HGDP1kGAC_asj gnomAD HGDP+1kG Ashkenazi Jewish AC - filterByRange.HGDP1kGAC_eas on - filterLabel.HGDP1kGAC_eas gnomAD HGDP+1kG East Asian AC - filterByRange.HGDP1kGAC_fin on - filterLabel.HGDP1kGAC_fin gnomAD HGDP+1kG Finnish AC - filterByRange.HGDP1kGAC_mid on - filterLabel.HGDP1kGAC_mid gnomAD HGDP+1kG Middle Eastern AC - filterByRange.HGDP1kGAC_nfe on - filterLabel.HGDP1kGAC_nfe gnomAD HGDP+1kG Non-Finnish European AC - filterByRange.HGDP1kGAC_oth on - filterLabel.HGDP1kGAC_oth gnomAD HGDP+1kG Other AC - filterByRange.HGDP1kGAC_sas on - filterLabel.HGDP1kGAC_sas gnomAD HGDP+1kG South Asian AC + # filterByRange.HGDP1kGAF_afr on + # filterLabel.HGDP1kGAF_afr gnomAD HGDP+1kG African AF + # filter.HGDP1kGAF_afr 0:1 + # filterLimits.HGDP1kGAF_afr 0:1 + # filterByRange.HGDP1kGAF_ami on + # filterLabel.HGDP1kGAF_ami gnomAD HGDP+1kG Amish AF + # filter.HGDP1kGAF_ami 0:1 + # filterLimits.HGDP1kGAF_ami 0:1 + # filterByRange.HGDP1kGAF_amr on + # filterLabel.HGDP1kGAF_amr gnomAD HGDP+1kG Latino AF + # filter.HGDP1kGAF_amr 0:1 + # filterLimits.HGDP1kGAF_amr 0:1 + # filterByRange.HGDP1kGAF_asj on + # filterLabel.HGDP1kGAF_asj gnomAD HGDP+1kG Ashkenazi Jewish AF + # filter.HGDP1kGAF_asj 0:1 + # filterLimits.HGDP1kGAF_asj 0:1 + # filterByRange.HGDP1kGAF_eas on + # filterLabel.HGDP1kGAF_eas gnomAD HGDP+1kG East Asian AF + # filter.HGDP1kGAF_eas 0:1 + # filterLimits.HGDP1kGAF_eas 0:1 + # filterByRange.HGDP1kGAF_fin on + # filterLabel.HGDP1kGAF_fin gnomAD HGDP+1kG Finnish AF + # filter.HGDP1kGAF_fin 0:1 + # filterLimits.HGDP1kGAF_fin 0:1 + # filterByRange.HGDP1kGAF_mid on + # filterLabel.HGDP1kGAF_mid gnomAD HGDP+1kG Middle Eastern AF + # filter.HGDP1kGAF_mid 0:1 + # filterLimits.HGDP1kGAF_mid 0:1 + # filterByRange.HGDP1kGAF_nfe on + # filterLabel.HGDP1kGAF_nfe gnomAD HGDP+1kG Non-Finnish European AF + # filter.HGDP1kGAF_nfe 0:1 + # filterLimits.HGDP1kGAF_nfe 0:1 + # filterByRange.HGDP1kGAF_oth on + # filterLabel.HGDP1kGAF_oth gnomAD HGDP+1kG Other AF + # filter.HGDP1kGAF_oth 0:1 + # filterLimits.HGDP1kGAF_oth 0:1 + # filterByRange.HGDP1kGAF_sas on + # filterLabel.HGDP1kGAF_sas gnomAD HGDP+1kG South Asian AF + # filter.HGDP1kGAF_sas 0:1 + # filterLimits.HGDP1kGAF_sas 0:1 + # filterByRange.HGDP1kGAC_afr on + # filterLabel.HGDP1kGAC_afr gnomAD HGDP+1kG African AC + # filter.HGDP1kGAC_afr 0:2000000 + # filterLimits.HGDP1kGAC_afr 0:2000000 + # filterByRange.HGDP1kGAC_ami on + # filterLabel.HGDP1kGAC_ami gnomAD HGDP+1kG Amish AC + # filter.HGDP1kGAC_ami 0:2000000 + # filterLimits.HGDP1kGAC_ami 0:2000000 + # filterByRange.HGDP1kGAC_amr on + # filterLabel.HGDP1kGAC_amr gnomAD HGDP+1kG Latino AC + # filter.HGDP1kGAC_amr 0:2000000 + # filterLimits.HGDP1kGAC_amr 0:2000000 + # filterByRange.HGDP1kGAC_asj on + # filterLabel.HGDP1kGAC_asj gnomAD HGDP+1kG Ashkenazi Jewish AC + # filter.HGDP1kGAC_asj 0:2000000 + # filterLimits.HGDP1kGAC_asj 0:2000000 + # filterByRange.HGDP1kGAC_eas on + # filterLabel.HGDP1kGAC_eas gnomAD HGDP+1kG East Asian AC + # filter.HGDP1kGAC_eas 0:2000000 + # filterLimits.HGDP1kGAC_eas 0:2000000 + # filterByRange.HGDP1kGAC_fin on + # filterLabel.HGDP1kGAC_fin gnomAD HGDP+1kG Finnish AC + # filter.HGDP1kGAC_fin 0:2000000 + # filterLimits.HGDP1kGAC_fin 0:2000000 + # filterByRange.HGDP1kGAC_mid on + # filterLabel.HGDP1kGAC_mid gnomAD HGDP+1kG Middle Eastern AC + # filter.HGDP1kGAC_mid 0:2000000 + # filterLimits.HGDP1kGAC_mid 0:2000000 + # filterByRange.HGDP1kGAC_nfe on + # filterLabel.HGDP1kGAC_nfe gnomAD HGDP+1kG Non-Finnish European AC + # filter.HGDP1kGAC_nfe 0:2000000 + # filterLimits.HGDP1kGAC_nfe 0:2000000 + # filterByRange.HGDP1kGAC_oth on + # filterLabel.HGDP1kGAC_oth gnomAD HGDP+1kG Other AC + # filter.HGDP1kGAC_oth 0:2000000 + # filterLimits.HGDP1kGAC_oth 0:2000000 + # filterByRange.HGDP1kGAC_sas on + # filterLabel.HGDP1kGAC_sas gnomAD HGDP+1kG South Asian AC + # filter.HGDP1kGAC_sas 0:2000000 + # filterLimits.HGDP1kGAC_sas 0:2000000 # GREGoR populations - filterByRange.GREGoRAF_AFF on - filterLabel.GREGoRAF_AFF GREGoR Affected AF - filterByRange.GREGoRAF_UNA on - filterLabel.GREGoRAF_UNA GREGoR Unaffected AF - filterByRange.GREGoRAF_UNK on - filterLabel.GREGoRAF_UNK GREGoR Unknown AF - filterByRange.GREGoRAC_AFF on - filterLabel.GREGoRAC_AFF GREGoR Affected AC - filterByRange.GREGoRAC_UNA on - filterLabel.GREGoRAC_UNA GREGoR Unaffected AC - filterByRange.GREGoRAC_UNK on - filterLabel.GREGoRAC_UNK GREGoR Unknown AC + # filterByRange.GREGoRAF_AFF on + # filterLabel.GREGoRAF_AFF GREGoR Affected AF + # filter.GREGoRAF_AFF 0:1 + # filterLimits.GREGoRAF_AFF 0:1 + # filterByRange.GREGoRAF_UNA on + # filterLabel.GREGoRAF_UNA GREGoR Unaffected AF + # filter.GREGoRAF_UNA 0:1 + # filterLimits.GREGoRAF_UNA 0:1 + # filterByRange.GREGoRAF_UNK on + # filterLabel.GREGoRAF_UNK GREGoR Unknown AF + # filter.GREGoRAF_UNK 0:1 + # filterLimits.GREGoRAF_UNK 0:1 + # filterByRange.GREGoRAC_AFF on + # filterLabel.GREGoRAC_AFF GREGoR Affected AC + # filter.GREGoRAC_AFF 0:2000000 + # filterLimits.GREGoRAC_AFF 0:2000000 + # filterByRange.GREGoRAC_UNA on + # filterLabel.GREGoRAC_UNA GREGoR Unaffected AC + # filter.GREGoRAC_UNA 0:2000000 + # filterLimits.GREGoRAC_UNA 0:2000000 + # filterByRange.GREGoRAC_UNK on + # filterLabel.GREGoRAC_UNK GREGoR Unknown AC + # filter.GREGoRAC_UNK 0:2000000 + # filterLimits.GREGoRAC_UNK 0:2000000 # SCHEMA populations - filterByRange.SCHEMAAF_CASE on - filterLabel.SCHEMAAF_CASE SCHEMA Schizophrenia case AF - filterByRange.SCHEMAAF_CTRL on - filterLabel.SCHEMAAF_CTRL SCHEMA Control AF - filterByRange.SCHEMAAC_CASE on - filterLabel.SCHEMAAC_CASE SCHEMA Schizophrenia case AC - filterByRange.SCHEMAAC_CTRL on - filterLabel.SCHEMAAC_CTRL SCHEMA Control AC + # filterByRange.SCHEMAAF_CASE on + # filterLabel.SCHEMAAF_CASE SCHEMA Schizophrenia case AF + # filter.SCHEMAAF_CASE 0:1 + # filterLimits.SCHEMAAF_CASE 0:1 + # filterByRange.SCHEMAAF_CTRL on + # filterLabel.SCHEMAAF_CTRL SCHEMA Control AF + # filter.SCHEMAAF_CTRL 0:1 + # filterLimits.SCHEMAAF_CTRL 0:1 + # filterByRange.SCHEMAAC_CASE on + # filterLabel.SCHEMAAC_CASE SCHEMA Schizophrenia case AC + # filter.SCHEMAAC_CASE 0:2000000 + # filterLimits.SCHEMAAC_CASE 0:2000000 + # filterByRange.SCHEMAAC_CTRL on + # filterLabel.SCHEMAAC_CTRL SCHEMA Control AC + # filter.SCHEMAAC_CTRL 0:2000000 + # filterLimits.SCHEMAAC_CTRL 0:2000000 # WBBC China populations - filterByRange.WBBCAF_North on - filterLabel.WBBCAF_North WBBC China North Han AF - filterByRange.WBBCAF_Central on - filterLabel.WBBCAF_Central WBBC China Central Han AF - filterByRange.WBBCAF_South on - filterLabel.WBBCAF_South WBBC China South Han AF - filterByRange.WBBCAF_Lingnan on - filterLabel.WBBCAF_Lingnan WBBC China Lingnan Han AF - filterByRange.WBBCAC_North on - filterLabel.WBBCAC_North WBBC China North Han AC - filterByRange.WBBCAC_Central on - filterLabel.WBBCAC_Central WBBC China Central Han AC - filterByRange.WBBCAC_South on - filterLabel.WBBCAC_South WBBC China South Han AC - filterByRange.WBBCAC_Lingnan on - filterLabel.WBBCAC_Lingnan WBBC China Lingnan Han AC + # filterByRange.WBBCAF_North on + # filterLabel.WBBCAF_North WBBC China North Han AF + # filter.WBBCAF_North 0:1 + # filterLimits.WBBCAF_North 0:1 + # filterByRange.WBBCAF_Central on + # filterLabel.WBBCAF_Central WBBC China Central Han AF + # filter.WBBCAF_Central 0:1 + # filterLimits.WBBCAF_Central 0:1 + # filterByRange.WBBCAF_South on + # filterLabel.WBBCAF_South WBBC China South Han AF + # filter.WBBCAF_South 0:1 + # filterLimits.WBBCAF_South 0:1 + # filterByRange.WBBCAF_Lingnan on + # filterLabel.WBBCAF_Lingnan WBBC China Lingnan Han AF + # filter.WBBCAF_Lingnan 0:1 + # filterLimits.WBBCAF_Lingnan 0:1 + # filterByRange.WBBCAC_North on + # filterLabel.WBBCAC_North WBBC China North Han AC + # filter.WBBCAC_North 0:2000000 + # filterLimits.WBBCAC_North 0:2000000 + # filterByRange.WBBCAC_Central on + # filterLabel.WBBCAC_Central WBBC China Central Han AC + # filter.WBBCAC_Central 0:2000000 + # filterLimits.WBBCAC_Central 0:2000000 + # filterByRange.WBBCAC_South on + # filterLabel.WBBCAC_South WBBC China South Han AC + # filter.WBBCAC_South 0:2000000 + # filterLimits.WBBCAC_South 0:2000000 + # filterByRange.WBBCAC_Lingnan on + # filterLabel.WBBCAC_Lingnan WBBC China Lingnan Han AC + # filter.WBBCAC_Lingnan 0:2000000 + # filterLimits.WBBCAC_Lingnan 0:2000000 skipEmptyFields on track varFreqsBackground shortLabel Population reference longLabel SNV Frequencies: variants in ~1.5 million individuals from population cohorts and unaffected or control arms type bigBed 9 + parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/_background/varFreqsBackground.bb tableBrowser off visibility pack itemRgb on maxWindowToDraw 5000000 priority 0.1 mouseOver <b>Var:</b> ${name}<br><b>AA change:</b> ${aaChange}<br><b>Var type:</b> ${varType}<br><b>Conseq:</b> ${consequence}<br><b>Background AF:</b> ${backgroundAF}<br><b>Background AC/AN:</b> ${backgroundAC} / ${backgroundAN}<br><b>Sources:</b> ${backgroundSources}<br><b>Affected AF:</b> ${affectedAF} filterValues.affectedCohorts SPARK|SFARI SPARK WES,SFARI_WGS|SFARI SPARK WGS,GREGoR|GREGoR,SCHEMA|SCHEMA,GA4K|GA4K PacBio LR filterType.affectedCohorts multipleListOr filterLabel.affectedCohorts Affected/case cohort filterValues.backgroundSources AllOfUs|AllOfUs,SPARK|SFARI SPARK WES,SFARI_WGS|SFARI SPARK WGS,GenomeAsia|GenomeAsia SNVs,GenomeAsiaIndel|GenomeAsia Indels,NPM|NPM Singapore,KOVA|KOVA Korea,ToMMo|ToMMo Japan,FinnGen|FinnGen Finland,Saudi|Saudi,SweGen|SweGen Sweden,TOPMed|TOPMed,ABraOM|ABraOM Brazil,ALFA|ALFA,MGRB|MGRB Australia,HRC|HRC,SGDP|SGDP,HGDP1kG|gnomAD HGDP+1kG,GREGoR|GREGoR,SCHEMA|SCHEMA,CoLoRSdb|CoLoRSdb PacBio LR,SVatalog|SVatalog 101 10XG SR,Tishkoff180|Tishkoff 180 African WGS,WBBC|WBBC China,ChinaMAP|China ChinaMAP,GenomeIndia|GenomeIndia 9.7k WGS,GoNL|GoNL Netherlands ~13x SR filterType.backgroundSources multipleListOr filterLabel.backgroundSources Background source (population or unaffected) # Variant type and consequence filters filterValues.varType SNV|SNV,INS|Insertion,DEL|Deletion,MNV|MNV filterLabel.varType Variant Type filterValues.consequence missense|Missense,synonymous|Synonymous,stop_gained|Stop Gained,frameshift|Frameshift,splice_donor|Splice Donor,splice_acceptor|Splice Acceptor,intron|Intron,3_prime_utr|3' UTR,5_prime_utr|5' UTR,non_coding|Non-coding,.|Intergenic,others|Other filterType.consequence multipleListOr filterLabel.consequence Consequence # Length filters filterByRange.refLen on filterLabel.refLen Reference Length filter.refLen 1:28037 filterLimits.refLen 1:28037 filterByRange.altLen on filterLabel.altLen Alternate Length filter.altLen 1:6294 filterLimits.altLen 1:6294 filterByRange.varLen on filterLabel.varLen Length Change filter.varLen -28036:6293 filterLimits.varLen -28036:6293 # Affected/case frequency summary filterByRange.affectedAF on filterLabel.affectedAF Affected/case AF (pooled) + filter.affectedAF 0:1 filterLimits.affectedAF 0:1 filterByRange.affectedAC on filterLabel.affectedAC Affected/case AC + filter.affectedAC 0:500000 + filterLimits.affectedAC 0:500000 filterByRange.affectedAN on filterLabel.affectedAN Affected/case AN (pool denominator) + filter.affectedAN 0:500000 + filterLimits.affectedAN 0:500000 # Background (population + unaffected) frequency summary filterByRange.backgroundAF on filterLabel.backgroundAF Background AF (pooled) + filter.backgroundAF 0:1 filterLimits.backgroundAF 0:1 filterByRange.backgroundAC on filterLabel.backgroundAC Background AC (population + unaffected) + filter.backgroundAC 0:5000000 + filterLimits.backgroundAC 0:5000000 filterByRange.backgroundAN on filterLabel.backgroundAN Background AN (pool denominator) + filter.backgroundAN 0:5000000 + filterLimits.backgroundAN 0:5000000 # Affected/case membership flag filterByRange.inAffected on filterLabel.inAffected Seen in an affected/case arm (1=yes, 0=no) filter.inAffected 0:1 filterLimits.inAffected 0:1 - # Per-database AF filters - filterByRange.AllOfUsAF on - filterLabel.AllOfUsAF AllOfUs AF - filterByRange.SPARKAF on - filterLabel.SPARKAF SFARI SPARK WES AF - filterByRange.SFARI_WGSAF on - filterLabel.SFARI_WGSAF SFARI SPARK WGS AF - filterByRange.GenomeAsiaAF on - filterLabel.GenomeAsiaAF GenomeAsia SNVs AF - filterByRange.GenomeAsiaIndelAF on - filterLabel.GenomeAsiaIndelAF GenomeAsia Indels AF - filterByRange.NPMAF on - filterLabel.NPMAF NPM Singapore AF - filterByRange.KOVAAF on - filterLabel.KOVAAF KOVA Korea AF - filterByRange.ToMMoAF on - filterLabel.ToMMoAF ToMMo Japan AF - filterByRange.FinnGenAF on - filterLabel.FinnGenAF FinnGen Finland AF - filterByRange.SaudiAF on - filterLabel.SaudiAF Saudi AF - filterByRange.SweGenAF on - filterLabel.SweGenAF SweGen Sweden AF - filterByRange.TOPMedAF on - filterLabel.TOPMedAF TOPMed AF - filterByRange.ABraOMAF on - filterLabel.ABraOMAF ABraOM Brazil AF - filterByRange.ALFAAF on - filterLabel.ALFAAF ALFA AF - filterByRange.MGRBAF on - filterLabel.MGRBAF MGRB Australia AF - filterByRange.HRCAF on - filterLabel.HRCAF HRC AF - filterByRange.SGDPAF on - filterLabel.SGDPAF SGDP AF - filterByRange.HGDP1kGAF on - filterLabel.HGDP1kGAF gnomAD HGDP+1kG AF - filterByRange.GREGoRAF on - filterLabel.GREGoRAF GREGoR AF - filterByRange.SCHEMAAF on - filterLabel.SCHEMAAF SCHEMA AF - filterByRange.GA4KAF on - filterLabel.GA4KAF GA4K PacBio LR AF - filterByRange.CoLoRSdbAF on - filterLabel.CoLoRSdbAF CoLoRSdb PacBio LR AF - filterByRange.SVatalogAF on - filterLabel.SVatalogAF SVatalog 101 10XG SR AF - filterByRange.Tishkoff180AF on - filterLabel.Tishkoff180AF Tishkoff 180 African WGS AF - filterByRange.WBBCAF on - filterLabel.WBBCAF WBBC China AF - filterByRange.ChinaMAPAF on - filterLabel.ChinaMAPAF China ChinaMAP AF - filterByRange.GenomeIndiaAF on - filterLabel.GenomeIndiaAF GenomeIndia 9.7k WGS AF - filterByRange.GoNLAF on - filterLabel.GoNLAF GoNL Netherlands ~13x SR AF - # Per-database AC filters - filterByRange.AllOfUsAC on - filterLabel.AllOfUsAC AllOfUs AC - filterByRange.SPARKAC on - filterLabel.SPARKAC SFARI SPARK WES AC - filterByRange.SFARI_WGSAC on - filterLabel.SFARI_WGSAC SFARI SPARK WGS AC - filterByRange.GenomeAsiaAC on - filterLabel.GenomeAsiaAC GenomeAsia SNVs AC - filterByRange.GenomeAsiaIndelAC on - filterLabel.GenomeAsiaIndelAC GenomeAsia Indels AC - filterByRange.NPMAC on - filterLabel.NPMAC NPM Singapore AC - filterByRange.KOVAAC on - filterLabel.KOVAAC KOVA Korea AC - filterByRange.ToMMoAC on - filterLabel.ToMMoAC ToMMo Japan AC - filterByRange.FinnGenAC on - filterLabel.FinnGenAC FinnGen Finland AC - filterByRange.SaudiAC on - filterLabel.SaudiAC Saudi AC - filterByRange.SweGenAC on - filterLabel.SweGenAC SweGen Sweden AC - filterByRange.TOPMedAC on - filterLabel.TOPMedAC TOPMed AC - filterByRange.ABraOMAC on - filterLabel.ABraOMAC ABraOM Brazil AC - filterByRange.ALFAAC on - filterLabel.ALFAAC ALFA AC - filterByRange.MGRBAC on - filterLabel.MGRBAC MGRB Australia AC - filterByRange.HRCAC on - filterLabel.HRCAC HRC AC - filterByRange.SGDPAC on - filterLabel.SGDPAC SGDP AC - filterByRange.HGDP1kGAC on - filterLabel.HGDP1kGAC gnomAD HGDP+1kG AC - filterByRange.GREGoRAC on - filterLabel.GREGoRAC GREGoR AC - filterByRange.SCHEMAAC on - filterLabel.SCHEMAAC SCHEMA AC - filterByRange.GA4KAC on - filterLabel.GA4KAC GA4K PacBio LR AC - filterByRange.CoLoRSdbAC on - filterLabel.CoLoRSdbAC CoLoRSdb PacBio LR AC - filterByRange.SVatalogAC on - filterLabel.SVatalogAC SVatalog 101 10XG SR AC - filterByRange.Tishkoff180AC on - filterLabel.Tishkoff180AC Tishkoff 180 African WGS AC - filterByRange.WBBCAC on - filterLabel.WBBCAC WBBC China AC - filterByRange.ChinaMAPAC on - filterLabel.ChinaMAPAC China ChinaMAP AC - filterByRange.GenomeIndiaAC on - filterLabel.GenomeIndiaAC GenomeIndia 9.7k WGS AC - filterByRange.GoNLAC on - filterLabel.GoNLAC GoNL Netherlands ~13x SR AC - # Population-specific AF filters + # Per-database AF filters (commented out: re-enable as needed) + # filterByRange.AllOfUsAF on + # filterLabel.AllOfUsAF AllOfUs AF + # filter.AllOfUsAF 0:1 + # filterLimits.AllOfUsAF 0:1 + # filterByRange.SPARKAF on + # filterLabel.SPARKAF SFARI SPARK WES AF + # filter.SPARKAF 0:1 + # filterLimits.SPARKAF 0:1 + # filterByRange.SFARI_WGSAF on + # filterLabel.SFARI_WGSAF SFARI SPARK WGS AF + # filter.SFARI_WGSAF 0:1 + # filterLimits.SFARI_WGSAF 0:1 + # filterByRange.GenomeAsiaAF on + # filterLabel.GenomeAsiaAF GenomeAsia SNVs AF + # filter.GenomeAsiaAF 0:1 + # filterLimits.GenomeAsiaAF 0:1 + # filterByRange.GenomeAsiaIndelAF on + # filterLabel.GenomeAsiaIndelAF GenomeAsia Indels AF + # filter.GenomeAsiaIndelAF 0:1 + # filterLimits.GenomeAsiaIndelAF 0:1 + # filterByRange.NPMAF on + # filterLabel.NPMAF NPM Singapore AF + # filter.NPMAF 0:1 + # filterLimits.NPMAF 0:1 + # filterByRange.KOVAAF on + # filterLabel.KOVAAF KOVA Korea AF + # filter.KOVAAF 0:1 + # filterLimits.KOVAAF 0:1 + # filterByRange.ToMMoAF on + # filterLabel.ToMMoAF ToMMo Japan AF + # filter.ToMMoAF 0:1 + # filterLimits.ToMMoAF 0:1 + # filterByRange.FinnGenAF on + # filterLabel.FinnGenAF FinnGen Finland AF + # filter.FinnGenAF 0:1 + # filterLimits.FinnGenAF 0:1 + # filterByRange.SaudiAF on + # filterLabel.SaudiAF Saudi AF + # filter.SaudiAF 0:1 + # filterLimits.SaudiAF 0:1 + # filterByRange.SweGenAF on + # filterLabel.SweGenAF SweGen Sweden AF + # filter.SweGenAF 0:1 + # filterLimits.SweGenAF 0:1 + # filterByRange.TOPMedAF on + # filterLabel.TOPMedAF TOPMed AF + # filter.TOPMedAF 0:1 + # filterLimits.TOPMedAF 0:1 + # filterByRange.ABraOMAF on + # filterLabel.ABraOMAF ABraOM Brazil AF + # filter.ABraOMAF 0:1 + # filterLimits.ABraOMAF 0:1 + # filterByRange.ALFAAF on + # filterLabel.ALFAAF ALFA AF + # filter.ALFAAF 0:1 + # filterLimits.ALFAAF 0:1 + # filterByRange.MGRBAF on + # filterLabel.MGRBAF MGRB Australia AF + # filter.MGRBAF 0:1 + # filterLimits.MGRBAF 0:1 + # filterByRange.HRCAF on + # filterLabel.HRCAF HRC AF + # filter.HRCAF 0:1 + # filterLimits.HRCAF 0:1 + # filterByRange.SGDPAF on + # filterLabel.SGDPAF SGDP AF + # filter.SGDPAF 0:1 + # filterLimits.SGDPAF 0:1 + # filterByRange.HGDP1kGAF on + # filterLabel.HGDP1kGAF gnomAD HGDP+1kG AF + # filter.HGDP1kGAF 0:1 + # filterLimits.HGDP1kGAF 0:1 + # filterByRange.GREGoRAF on + # filterLabel.GREGoRAF GREGoR AF + # filter.GREGoRAF 0:1 + # filterLimits.GREGoRAF 0:1 + # filterByRange.SCHEMAAF on + # filterLabel.SCHEMAAF SCHEMA AF + # filter.SCHEMAAF 0:1 + # filterLimits.SCHEMAAF 0:1 + # filterByRange.GA4KAF on + # filterLabel.GA4KAF GA4K PacBio LR AF + # filter.GA4KAF 0:1 + # filterLimits.GA4KAF 0:1 + # filterByRange.CoLoRSdbAF on + # filterLabel.CoLoRSdbAF CoLoRSdb PacBio LR AF + # filter.CoLoRSdbAF 0:1 + # filterLimits.CoLoRSdbAF 0:1 + # filterByRange.SVatalogAF on + # filterLabel.SVatalogAF SVatalog 101 10XG SR AF + # filter.SVatalogAF 0:1 + # filterLimits.SVatalogAF 0:1 + # filterByRange.Tishkoff180AF on + # filterLabel.Tishkoff180AF Tishkoff 180 African WGS AF + # filter.Tishkoff180AF 0:1 + # filterLimits.Tishkoff180AF 0:1 + # filterByRange.WBBCAF on + # filterLabel.WBBCAF WBBC China AF + # filter.WBBCAF 0:1 + # filterLimits.WBBCAF 0:1 + # filterByRange.ChinaMAPAF on + # filterLabel.ChinaMAPAF China ChinaMAP AF + # filter.ChinaMAPAF 0:1 + # filterLimits.ChinaMAPAF 0:1 + # filterByRange.GenomeIndiaAF on + # filterLabel.GenomeIndiaAF GenomeIndia 9.7k WGS AF + # filter.GenomeIndiaAF 0:1 + # filterLimits.GenomeIndiaAF 0:1 + # filterByRange.GoNLAF on + # filterLabel.GoNLAF GoNL Netherlands ~13x SR AF + # filter.GoNLAF 0:1 + # filterLimits.GoNLAF 0:1 + # Per-database AC filters (commented out: re-enable as needed) + # filterByRange.AllOfUsAC on + # filterLabel.AllOfUsAC AllOfUs AC + # filter.AllOfUsAC 0:2000000 + # filterLimits.AllOfUsAC 0:2000000 + # filterByRange.SPARKAC on + # filterLabel.SPARKAC SFARI SPARK WES AC + # filter.SPARKAC 0:2000000 + # filterLimits.SPARKAC 0:2000000 + # filterByRange.SFARI_WGSAC on + # filterLabel.SFARI_WGSAC SFARI SPARK WGS AC + # filter.SFARI_WGSAC 0:2000000 + # filterLimits.SFARI_WGSAC 0:2000000 + # filterByRange.GenomeAsiaAC on + # filterLabel.GenomeAsiaAC GenomeAsia SNVs AC + # filter.GenomeAsiaAC 0:2000000 + # filterLimits.GenomeAsiaAC 0:2000000 + # filterByRange.GenomeAsiaIndelAC on + # filterLabel.GenomeAsiaIndelAC GenomeAsia Indels AC + # filter.GenomeAsiaIndelAC 0:2000000 + # filterLimits.GenomeAsiaIndelAC 0:2000000 + # filterByRange.NPMAC on + # filterLabel.NPMAC NPM Singapore AC + # filter.NPMAC 0:2000000 + # filterLimits.NPMAC 0:2000000 + # filterByRange.KOVAAC on + # filterLabel.KOVAAC KOVA Korea AC + # filter.KOVAAC 0:2000000 + # filterLimits.KOVAAC 0:2000000 + # filterByRange.ToMMoAC on + # filterLabel.ToMMoAC ToMMo Japan AC + # filter.ToMMoAC 0:2000000 + # filterLimits.ToMMoAC 0:2000000 + # filterByRange.FinnGenAC on + # filterLabel.FinnGenAC FinnGen Finland AC + # filter.FinnGenAC 0:2000000 + # filterLimits.FinnGenAC 0:2000000 + # filterByRange.SaudiAC on + # filterLabel.SaudiAC Saudi AC + # filter.SaudiAC 0:2000000 + # filterLimits.SaudiAC 0:2000000 + # filterByRange.SweGenAC on + # filterLabel.SweGenAC SweGen Sweden AC + # filter.SweGenAC 0:2000000 + # filterLimits.SweGenAC 0:2000000 + # filterByRange.TOPMedAC on + # filterLabel.TOPMedAC TOPMed AC + # filter.TOPMedAC 0:2000000 + # filterLimits.TOPMedAC 0:2000000 + # filterByRange.ABraOMAC on + # filterLabel.ABraOMAC ABraOM Brazil AC + # filter.ABraOMAC 0:2000000 + # filterLimits.ABraOMAC 0:2000000 + # filterByRange.ALFAAC on + # filterLabel.ALFAAC ALFA AC + # filter.ALFAAC 0:2000000 + # filterLimits.ALFAAC 0:2000000 + # filterByRange.MGRBAC on + # filterLabel.MGRBAC MGRB Australia AC + # filter.MGRBAC 0:2000000 + # filterLimits.MGRBAC 0:2000000 + # filterByRange.HRCAC on + # filterLabel.HRCAC HRC AC + # filter.HRCAC 0:2000000 + # filterLimits.HRCAC 0:2000000 + # filterByRange.SGDPAC on + # filterLabel.SGDPAC SGDP AC + # filter.SGDPAC 0:2000000 + # filterLimits.SGDPAC 0:2000000 + # filterByRange.HGDP1kGAC on + # filterLabel.HGDP1kGAC gnomAD HGDP+1kG AC + # filter.HGDP1kGAC 0:2000000 + # filterLimits.HGDP1kGAC 0:2000000 + # filterByRange.GREGoRAC on + # filterLabel.GREGoRAC GREGoR AC + # filter.GREGoRAC 0:2000000 + # filterLimits.GREGoRAC 0:2000000 + # filterByRange.SCHEMAAC on + # filterLabel.SCHEMAAC SCHEMA AC + # filter.SCHEMAAC 0:2000000 + # filterLimits.SCHEMAAC 0:2000000 + # filterByRange.GA4KAC on + # filterLabel.GA4KAC GA4K PacBio LR AC + # filter.GA4KAC 0:2000000 + # filterLimits.GA4KAC 0:2000000 + # filterByRange.CoLoRSdbAC on + # filterLabel.CoLoRSdbAC CoLoRSdb PacBio LR AC + # filter.CoLoRSdbAC 0:2000000 + # filterLimits.CoLoRSdbAC 0:2000000 + # filterByRange.SVatalogAC on + # filterLabel.SVatalogAC SVatalog 101 10XG SR AC + # filter.SVatalogAC 0:2000000 + # filterLimits.SVatalogAC 0:2000000 + # filterByRange.Tishkoff180AC on + # filterLabel.Tishkoff180AC Tishkoff 180 African WGS AC + # filter.Tishkoff180AC 0:2000000 + # filterLimits.Tishkoff180AC 0:2000000 + # filterByRange.WBBCAC on + # filterLabel.WBBCAC WBBC China AC + # filter.WBBCAC 0:2000000 + # filterLimits.WBBCAC 0:2000000 + # filterByRange.ChinaMAPAC on + # filterLabel.ChinaMAPAC China ChinaMAP AC + # filter.ChinaMAPAC 0:2000000 + # filterLimits.ChinaMAPAC 0:2000000 + # filterByRange.GenomeIndiaAC on + # filterLabel.GenomeIndiaAC GenomeIndia 9.7k WGS AC + # filter.GenomeIndiaAC 0:2000000 + # filterLimits.GenomeIndiaAC 0:2000000 + # filterByRange.GoNLAC on + # filterLabel.GoNLAC GoNL Netherlands ~13x SR AC + # filter.GoNLAC 0:2000000 + # filterLimits.GoNLAC 0:2000000 + # Population-specific AF/AC filters (commented out: re-enable as needed) # AllOfUs populations - filterByRange.AllOfUsAF_AFR on - filterLabel.AllOfUsAF_AFR AllOfUs African AF - filterByRange.AllOfUsAF_AMR on - filterLabel.AllOfUsAF_AMR AllOfUs Indigenous American AF - filterByRange.AllOfUsAF_EAS on - filterLabel.AllOfUsAF_EAS AllOfUs East Asian AF - filterByRange.AllOfUsAF_EUR on - filterLabel.AllOfUsAF_EUR AllOfUs European AF - filterByRange.AllOfUsAF_OCE on - filterLabel.AllOfUsAF_OCE AllOfUs Oceanian AF - filterByRange.AllOfUsAF_SAS on - filterLabel.AllOfUsAF_SAS AllOfUs South Asian AF - filterByRange.AllOfUsAC_AFR on - filterLabel.AllOfUsAC_AFR AllOfUs African AC - filterByRange.AllOfUsAC_AMR on - filterLabel.AllOfUsAC_AMR AllOfUs Indigenous American AC - filterByRange.AllOfUsAC_EAS on - filterLabel.AllOfUsAC_EAS AllOfUs East Asian AC - filterByRange.AllOfUsAC_EUR on - filterLabel.AllOfUsAC_EUR AllOfUs European AC - filterByRange.AllOfUsAC_OCE on - filterLabel.AllOfUsAC_OCE AllOfUs Oceanian AC - filterByRange.AllOfUsAC_SAS on - filterLabel.AllOfUsAC_SAS AllOfUs South Asian AC + # filterByRange.AllOfUsAF_AFR on + # filterLabel.AllOfUsAF_AFR AllOfUs African AF + # filter.AllOfUsAF_AFR 0:1 + # filterLimits.AllOfUsAF_AFR 0:1 + # filterByRange.AllOfUsAF_AMR on + # filterLabel.AllOfUsAF_AMR AllOfUs Indigenous American AF + # filter.AllOfUsAF_AMR 0:1 + # filterLimits.AllOfUsAF_AMR 0:1 + # filterByRange.AllOfUsAF_EAS on + # filterLabel.AllOfUsAF_EAS AllOfUs East Asian AF + # filter.AllOfUsAF_EAS 0:1 + # filterLimits.AllOfUsAF_EAS 0:1 + # filterByRange.AllOfUsAF_EUR on + # filterLabel.AllOfUsAF_EUR AllOfUs European AF + # filter.AllOfUsAF_EUR 0:1 + # filterLimits.AllOfUsAF_EUR 0:1 + # filterByRange.AllOfUsAF_OCE on + # filterLabel.AllOfUsAF_OCE AllOfUs Oceanian AF + # filter.AllOfUsAF_OCE 0:1 + # filterLimits.AllOfUsAF_OCE 0:1 + # filterByRange.AllOfUsAF_SAS on + # filterLabel.AllOfUsAF_SAS AllOfUs South Asian AF + # filter.AllOfUsAF_SAS 0:1 + # filterLimits.AllOfUsAF_SAS 0:1 + # filterByRange.AllOfUsAC_AFR on + # filterLabel.AllOfUsAC_AFR AllOfUs African AC + # filter.AllOfUsAC_AFR 0:2000000 + # filterLimits.AllOfUsAC_AFR 0:2000000 + # filterByRange.AllOfUsAC_AMR on + # filterLabel.AllOfUsAC_AMR AllOfUs Indigenous American AC + # filter.AllOfUsAC_AMR 0:2000000 + # filterLimits.AllOfUsAC_AMR 0:2000000 + # filterByRange.AllOfUsAC_EAS on + # filterLabel.AllOfUsAC_EAS AllOfUs East Asian AC + # filter.AllOfUsAC_EAS 0:2000000 + # filterLimits.AllOfUsAC_EAS 0:2000000 + # filterByRange.AllOfUsAC_EUR on + # filterLabel.AllOfUsAC_EUR AllOfUs European AC + # filter.AllOfUsAC_EUR 0:2000000 + # filterLimits.AllOfUsAC_EUR 0:2000000 + # filterByRange.AllOfUsAC_OCE on + # filterLabel.AllOfUsAC_OCE AllOfUs Oceanian AC + # filter.AllOfUsAC_OCE 0:2000000 + # filterLimits.AllOfUsAC_OCE 0:2000000 + # filterByRange.AllOfUsAC_SAS on + # filterLabel.AllOfUsAC_SAS AllOfUs South Asian AC + # filter.AllOfUsAC_SAS 0:2000000 + # filterLimits.AllOfUsAC_SAS 0:2000000 # SFARI SPARK WES populations - filterByRange.SPARKAF_AUT on - filterLabel.SPARKAF_AUT SFARI SPARK WES ASD proband AF - filterByRange.SPARKAF_NON_AUT on - filterLabel.SPARKAF_NON_AUT SFARI SPARK WES Non-ASD family AF - filterByRange.SPARKAC_AUT on - filterLabel.SPARKAC_AUT SFARI SPARK WES ASD proband AC - filterByRange.SPARKAC_NON_AUT on - filterLabel.SPARKAC_NON_AUT SFARI SPARK WES Non-ASD family AC + # filterByRange.SPARKAF_AUT on + # filterLabel.SPARKAF_AUT SFARI SPARK WES ASD proband AF + # filter.SPARKAF_AUT 0:1 + # filterLimits.SPARKAF_AUT 0:1 + # filterByRange.SPARKAF_NON_AUT on + # filterLabel.SPARKAF_NON_AUT SFARI SPARK WES Non-ASD family AF + # filter.SPARKAF_NON_AUT 0:1 + # filterLimits.SPARKAF_NON_AUT 0:1 + # filterByRange.SPARKAC_AUT on + # filterLabel.SPARKAC_AUT SFARI SPARK WES ASD proband AC + # filter.SPARKAC_AUT 0:2000000 + # filterLimits.SPARKAC_AUT 0:2000000 + # filterByRange.SPARKAC_NON_AUT on + # filterLabel.SPARKAC_NON_AUT SFARI SPARK WES Non-ASD family AC + # filter.SPARKAC_NON_AUT 0:2000000 + # filterLimits.SPARKAC_NON_AUT 0:2000000 # SFARI SPARK WGS populations - filterByRange.SFARI_WGSAF_AUT on - filterLabel.SFARI_WGSAF_AUT SFARI SPARK WGS ASD proband AF - filterByRange.SFARI_WGSAF_NON_AUT on - filterLabel.SFARI_WGSAF_NON_AUT SFARI SPARK WGS Non-ASD family AF - filterByRange.SFARI_WGSAC_AUT on - filterLabel.SFARI_WGSAC_AUT SFARI SPARK WGS ASD proband AC - filterByRange.SFARI_WGSAC_NON_AUT on - filterLabel.SFARI_WGSAC_NON_AUT SFARI SPARK WGS Non-ASD family AC + # filterByRange.SFARI_WGSAF_AUT on + # filterLabel.SFARI_WGSAF_AUT SFARI SPARK WGS ASD proband AF + # filter.SFARI_WGSAF_AUT 0:1 + # filterLimits.SFARI_WGSAF_AUT 0:1 + # filterByRange.SFARI_WGSAF_NON_AUT on + # filterLabel.SFARI_WGSAF_NON_AUT SFARI SPARK WGS Non-ASD family AF + # filter.SFARI_WGSAF_NON_AUT 0:1 + # filterLimits.SFARI_WGSAF_NON_AUT 0:1 + # filterByRange.SFARI_WGSAC_AUT on + # filterLabel.SFARI_WGSAC_AUT SFARI SPARK WGS ASD proband AC + # filter.SFARI_WGSAC_AUT 0:2000000 + # filterLimits.SFARI_WGSAC_AUT 0:2000000 + # filterByRange.SFARI_WGSAC_NON_AUT on + # filterLabel.SFARI_WGSAC_NON_AUT SFARI SPARK WGS Non-ASD family AC + # filter.SFARI_WGSAC_NON_AUT 0:2000000 + # filterLimits.SFARI_WGSAC_NON_AUT 0:2000000 # GenomeAsia SNVs populations - filterByRange.GenomeAsiaAF_NEA on - filterLabel.GenomeAsiaAF_NEA GenomeAsia SNVs Northeast Asian AF - filterByRange.GenomeAsiaAF_SEA on - filterLabel.GenomeAsiaAF_SEA GenomeAsia SNVs Southeast Asian AF - filterByRange.GenomeAsiaAF_SAS on - filterLabel.GenomeAsiaAF_SAS GenomeAsia SNVs South Asian AF - filterByRange.GenomeAsiaAF_OCE on - filterLabel.GenomeAsiaAF_OCE GenomeAsia SNVs Oceanian AF - filterByRange.GenomeAsiaAF_AMR on - filterLabel.GenomeAsiaAF_AMR GenomeAsia SNVs American AF - filterByRange.GenomeAsiaAF_AFR on - filterLabel.GenomeAsiaAF_AFR GenomeAsia SNVs African AF - filterByRange.GenomeAsiaAF_WER on - filterLabel.GenomeAsiaAF_WER GenomeAsia SNVs Western European Ref AF - filterByRange.GenomeAsiaAC_NEA on - filterLabel.GenomeAsiaAC_NEA GenomeAsia SNVs Northeast Asian AC - filterByRange.GenomeAsiaAC_SEA on - filterLabel.GenomeAsiaAC_SEA GenomeAsia SNVs Southeast Asian AC - filterByRange.GenomeAsiaAC_SAS on - filterLabel.GenomeAsiaAC_SAS GenomeAsia SNVs South Asian AC - filterByRange.GenomeAsiaAC_OCE on - filterLabel.GenomeAsiaAC_OCE GenomeAsia SNVs Oceanian AC - filterByRange.GenomeAsiaAC_AMR on - filterLabel.GenomeAsiaAC_AMR GenomeAsia SNVs American AC - filterByRange.GenomeAsiaAC_AFR on - filterLabel.GenomeAsiaAC_AFR GenomeAsia SNVs African AC - filterByRange.GenomeAsiaAC_WER on - filterLabel.GenomeAsiaAC_WER GenomeAsia SNVs Western European Ref AC + # filterByRange.GenomeAsiaAF_NEA on + # filterLabel.GenomeAsiaAF_NEA GenomeAsia SNVs Northeast Asian AF + # filter.GenomeAsiaAF_NEA 0:1 + # filterLimits.GenomeAsiaAF_NEA 0:1 + # filterByRange.GenomeAsiaAF_SEA on + # filterLabel.GenomeAsiaAF_SEA GenomeAsia SNVs Southeast Asian AF + # filter.GenomeAsiaAF_SEA 0:1 + # filterLimits.GenomeAsiaAF_SEA 0:1 + # filterByRange.GenomeAsiaAF_SAS on + # filterLabel.GenomeAsiaAF_SAS GenomeAsia SNVs South Asian AF + # filter.GenomeAsiaAF_SAS 0:1 + # filterLimits.GenomeAsiaAF_SAS 0:1 + # filterByRange.GenomeAsiaAF_OCE on + # filterLabel.GenomeAsiaAF_OCE GenomeAsia SNVs Oceanian AF + # filter.GenomeAsiaAF_OCE 0:1 + # filterLimits.GenomeAsiaAF_OCE 0:1 + # filterByRange.GenomeAsiaAF_AMR on + # filterLabel.GenomeAsiaAF_AMR GenomeAsia SNVs American AF + # filter.GenomeAsiaAF_AMR 0:1 + # filterLimits.GenomeAsiaAF_AMR 0:1 + # filterByRange.GenomeAsiaAF_AFR on + # filterLabel.GenomeAsiaAF_AFR GenomeAsia SNVs African AF + # filter.GenomeAsiaAF_AFR 0:1 + # filterLimits.GenomeAsiaAF_AFR 0:1 + # filterByRange.GenomeAsiaAF_WER on + # filterLabel.GenomeAsiaAF_WER GenomeAsia SNVs Western European Ref AF + # filter.GenomeAsiaAF_WER 0:1 + # filterLimits.GenomeAsiaAF_WER 0:1 + # filterByRange.GenomeAsiaAC_NEA on + # filterLabel.GenomeAsiaAC_NEA GenomeAsia SNVs Northeast Asian AC + # filter.GenomeAsiaAC_NEA 0:2000000 + # filterLimits.GenomeAsiaAC_NEA 0:2000000 + # filterByRange.GenomeAsiaAC_SEA on + # filterLabel.GenomeAsiaAC_SEA GenomeAsia SNVs Southeast Asian AC + # filter.GenomeAsiaAC_SEA 0:2000000 + # filterLimits.GenomeAsiaAC_SEA 0:2000000 + # filterByRange.GenomeAsiaAC_SAS on + # filterLabel.GenomeAsiaAC_SAS GenomeAsia SNVs South Asian AC + # filter.GenomeAsiaAC_SAS 0:2000000 + # filterLimits.GenomeAsiaAC_SAS 0:2000000 + # filterByRange.GenomeAsiaAC_OCE on + # filterLabel.GenomeAsiaAC_OCE GenomeAsia SNVs Oceanian AC + # filter.GenomeAsiaAC_OCE 0:2000000 + # filterLimits.GenomeAsiaAC_OCE 0:2000000 + # filterByRange.GenomeAsiaAC_AMR on + # filterLabel.GenomeAsiaAC_AMR GenomeAsia SNVs American AC + # filter.GenomeAsiaAC_AMR 0:2000000 + # filterLimits.GenomeAsiaAC_AMR 0:2000000 + # filterByRange.GenomeAsiaAC_AFR on + # filterLabel.GenomeAsiaAC_AFR GenomeAsia SNVs African AC + # filter.GenomeAsiaAC_AFR 0:2000000 + # filterLimits.GenomeAsiaAC_AFR 0:2000000 + # filterByRange.GenomeAsiaAC_WER on + # filterLabel.GenomeAsiaAC_WER GenomeAsia SNVs Western European Ref AC + # filter.GenomeAsiaAC_WER 0:2000000 + # filterLimits.GenomeAsiaAC_WER 0:2000000 # NPM Singapore populations - filterByRange.NPMAF_Chinese on - filterLabel.NPMAF_Chinese NPM Singapore Singapore Chinese AF - filterByRange.NPMAF_Malay on - filterLabel.NPMAF_Malay NPM Singapore Singapore Malay AF - filterByRange.NPMAF_Indian on - filterLabel.NPMAF_Indian NPM Singapore Singapore Indian AF - filterByRange.NPMAC_Chinese on - filterLabel.NPMAC_Chinese NPM Singapore Singapore Chinese AC - filterByRange.NPMAC_Malay on - filterLabel.NPMAC_Malay NPM Singapore Singapore Malay AC - filterByRange.NPMAC_Indian on - filterLabel.NPMAC_Indian NPM Singapore Singapore Indian AC + # filterByRange.NPMAF_Chinese on + # filterLabel.NPMAF_Chinese NPM Singapore Singapore Chinese AF + # filter.NPMAF_Chinese 0:1 + # filterLimits.NPMAF_Chinese 0:1 + # filterByRange.NPMAF_Malay on + # filterLabel.NPMAF_Malay NPM Singapore Singapore Malay AF + # filter.NPMAF_Malay 0:1 + # filterLimits.NPMAF_Malay 0:1 + # filterByRange.NPMAF_Indian on + # filterLabel.NPMAF_Indian NPM Singapore Singapore Indian AF + # filter.NPMAF_Indian 0:1 + # filterLimits.NPMAF_Indian 0:1 + # filterByRange.NPMAC_Chinese on + # filterLabel.NPMAC_Chinese NPM Singapore Singapore Chinese AC + # filter.NPMAC_Chinese 0:2000000 + # filterLimits.NPMAC_Chinese 0:2000000 + # filterByRange.NPMAC_Malay on + # filterLabel.NPMAC_Malay NPM Singapore Singapore Malay AC + # filter.NPMAC_Malay 0:2000000 + # filterLimits.NPMAC_Malay 0:2000000 + # filterByRange.NPMAC_Indian on + # filterLabel.NPMAC_Indian NPM Singapore Singapore Indian AC + # filter.NPMAC_Indian 0:2000000 + # filterLimits.NPMAC_Indian 0:2000000 # gnomAD HGDP+1kG populations - filterByRange.HGDP1kGAF_afr on - filterLabel.HGDP1kGAF_afr gnomAD HGDP+1kG African AF - filterByRange.HGDP1kGAF_ami on - filterLabel.HGDP1kGAF_ami gnomAD HGDP+1kG Amish AF - filterByRange.HGDP1kGAF_amr on - filterLabel.HGDP1kGAF_amr gnomAD HGDP+1kG Latino AF - filterByRange.HGDP1kGAF_asj on - filterLabel.HGDP1kGAF_asj gnomAD HGDP+1kG Ashkenazi Jewish AF - filterByRange.HGDP1kGAF_eas on - filterLabel.HGDP1kGAF_eas gnomAD HGDP+1kG East Asian AF - filterByRange.HGDP1kGAF_fin on - filterLabel.HGDP1kGAF_fin gnomAD HGDP+1kG Finnish AF - filterByRange.HGDP1kGAF_mid on - filterLabel.HGDP1kGAF_mid gnomAD HGDP+1kG Middle Eastern AF - filterByRange.HGDP1kGAF_nfe on - filterLabel.HGDP1kGAF_nfe gnomAD HGDP+1kG Non-Finnish European AF - filterByRange.HGDP1kGAF_oth on - filterLabel.HGDP1kGAF_oth gnomAD HGDP+1kG Other AF - filterByRange.HGDP1kGAF_sas on - filterLabel.HGDP1kGAF_sas gnomAD HGDP+1kG South Asian AF - filterByRange.HGDP1kGAC_afr on - filterLabel.HGDP1kGAC_afr gnomAD HGDP+1kG African AC - filterByRange.HGDP1kGAC_ami on - filterLabel.HGDP1kGAC_ami gnomAD HGDP+1kG Amish AC - filterByRange.HGDP1kGAC_amr on - filterLabel.HGDP1kGAC_amr gnomAD HGDP+1kG Latino AC - filterByRange.HGDP1kGAC_asj on - filterLabel.HGDP1kGAC_asj gnomAD HGDP+1kG Ashkenazi Jewish AC - filterByRange.HGDP1kGAC_eas on - filterLabel.HGDP1kGAC_eas gnomAD HGDP+1kG East Asian AC - filterByRange.HGDP1kGAC_fin on - filterLabel.HGDP1kGAC_fin gnomAD HGDP+1kG Finnish AC - filterByRange.HGDP1kGAC_mid on - filterLabel.HGDP1kGAC_mid gnomAD HGDP+1kG Middle Eastern AC - filterByRange.HGDP1kGAC_nfe on - filterLabel.HGDP1kGAC_nfe gnomAD HGDP+1kG Non-Finnish European AC - filterByRange.HGDP1kGAC_oth on - filterLabel.HGDP1kGAC_oth gnomAD HGDP+1kG Other AC - filterByRange.HGDP1kGAC_sas on - filterLabel.HGDP1kGAC_sas gnomAD HGDP+1kG South Asian AC + # filterByRange.HGDP1kGAF_afr on + # filterLabel.HGDP1kGAF_afr gnomAD HGDP+1kG African AF + # filter.HGDP1kGAF_afr 0:1 + # filterLimits.HGDP1kGAF_afr 0:1 + # filterByRange.HGDP1kGAF_ami on + # filterLabel.HGDP1kGAF_ami gnomAD HGDP+1kG Amish AF + # filter.HGDP1kGAF_ami 0:1 + # filterLimits.HGDP1kGAF_ami 0:1 + # filterByRange.HGDP1kGAF_amr on + # filterLabel.HGDP1kGAF_amr gnomAD HGDP+1kG Latino AF + # filter.HGDP1kGAF_amr 0:1 + # filterLimits.HGDP1kGAF_amr 0:1 + # filterByRange.HGDP1kGAF_asj on + # filterLabel.HGDP1kGAF_asj gnomAD HGDP+1kG Ashkenazi Jewish AF + # filter.HGDP1kGAF_asj 0:1 + # filterLimits.HGDP1kGAF_asj 0:1 + # filterByRange.HGDP1kGAF_eas on + # filterLabel.HGDP1kGAF_eas gnomAD HGDP+1kG East Asian AF + # filter.HGDP1kGAF_eas 0:1 + # filterLimits.HGDP1kGAF_eas 0:1 + # filterByRange.HGDP1kGAF_fin on + # filterLabel.HGDP1kGAF_fin gnomAD HGDP+1kG Finnish AF + # filter.HGDP1kGAF_fin 0:1 + # filterLimits.HGDP1kGAF_fin 0:1 + # filterByRange.HGDP1kGAF_mid on + # filterLabel.HGDP1kGAF_mid gnomAD HGDP+1kG Middle Eastern AF + # filter.HGDP1kGAF_mid 0:1 + # filterLimits.HGDP1kGAF_mid 0:1 + # filterByRange.HGDP1kGAF_nfe on + # filterLabel.HGDP1kGAF_nfe gnomAD HGDP+1kG Non-Finnish European AF + # filter.HGDP1kGAF_nfe 0:1 + # filterLimits.HGDP1kGAF_nfe 0:1 + # filterByRange.HGDP1kGAF_oth on + # filterLabel.HGDP1kGAF_oth gnomAD HGDP+1kG Other AF + # filter.HGDP1kGAF_oth 0:1 + # filterLimits.HGDP1kGAF_oth 0:1 + # filterByRange.HGDP1kGAF_sas on + # filterLabel.HGDP1kGAF_sas gnomAD HGDP+1kG South Asian AF + # filter.HGDP1kGAF_sas 0:1 + # filterLimits.HGDP1kGAF_sas 0:1 + # filterByRange.HGDP1kGAC_afr on + # filterLabel.HGDP1kGAC_afr gnomAD HGDP+1kG African AC + # filter.HGDP1kGAC_afr 0:2000000 + # filterLimits.HGDP1kGAC_afr 0:2000000 + # filterByRange.HGDP1kGAC_ami on + # filterLabel.HGDP1kGAC_ami gnomAD HGDP+1kG Amish AC + # filter.HGDP1kGAC_ami 0:2000000 + # filterLimits.HGDP1kGAC_ami 0:2000000 + # filterByRange.HGDP1kGAC_amr on + # filterLabel.HGDP1kGAC_amr gnomAD HGDP+1kG Latino AC + # filter.HGDP1kGAC_amr 0:2000000 + # filterLimits.HGDP1kGAC_amr 0:2000000 + # filterByRange.HGDP1kGAC_asj on + # filterLabel.HGDP1kGAC_asj gnomAD HGDP+1kG Ashkenazi Jewish AC + # filter.HGDP1kGAC_asj 0:2000000 + # filterLimits.HGDP1kGAC_asj 0:2000000 + # filterByRange.HGDP1kGAC_eas on + # filterLabel.HGDP1kGAC_eas gnomAD HGDP+1kG East Asian AC + # filter.HGDP1kGAC_eas 0:2000000 + # filterLimits.HGDP1kGAC_eas 0:2000000 + # filterByRange.HGDP1kGAC_fin on + # filterLabel.HGDP1kGAC_fin gnomAD HGDP+1kG Finnish AC + # filter.HGDP1kGAC_fin 0:2000000 + # filterLimits.HGDP1kGAC_fin 0:2000000 + # filterByRange.HGDP1kGAC_mid on + # filterLabel.HGDP1kGAC_mid gnomAD HGDP+1kG Middle Eastern AC + # filter.HGDP1kGAC_mid 0:2000000 + # filterLimits.HGDP1kGAC_mid 0:2000000 + # filterByRange.HGDP1kGAC_nfe on + # filterLabel.HGDP1kGAC_nfe gnomAD HGDP+1kG Non-Finnish European AC + # filter.HGDP1kGAC_nfe 0:2000000 + # filterLimits.HGDP1kGAC_nfe 0:2000000 + # filterByRange.HGDP1kGAC_oth on + # filterLabel.HGDP1kGAC_oth gnomAD HGDP+1kG Other AC + # filter.HGDP1kGAC_oth 0:2000000 + # filterLimits.HGDP1kGAC_oth 0:2000000 + # filterByRange.HGDP1kGAC_sas on + # filterLabel.HGDP1kGAC_sas gnomAD HGDP+1kG South Asian AC + # filter.HGDP1kGAC_sas 0:2000000 + # filterLimits.HGDP1kGAC_sas 0:2000000 # GREGoR populations - filterByRange.GREGoRAF_AFF on - filterLabel.GREGoRAF_AFF GREGoR Affected AF - filterByRange.GREGoRAF_UNA on - filterLabel.GREGoRAF_UNA GREGoR Unaffected AF - filterByRange.GREGoRAF_UNK on - filterLabel.GREGoRAF_UNK GREGoR Unknown AF - filterByRange.GREGoRAC_AFF on - filterLabel.GREGoRAC_AFF GREGoR Affected AC - filterByRange.GREGoRAC_UNA on - filterLabel.GREGoRAC_UNA GREGoR Unaffected AC - filterByRange.GREGoRAC_UNK on - filterLabel.GREGoRAC_UNK GREGoR Unknown AC + # filterByRange.GREGoRAF_AFF on + # filterLabel.GREGoRAF_AFF GREGoR Affected AF + # filter.GREGoRAF_AFF 0:1 + # filterLimits.GREGoRAF_AFF 0:1 + # filterByRange.GREGoRAF_UNA on + # filterLabel.GREGoRAF_UNA GREGoR Unaffected AF + # filter.GREGoRAF_UNA 0:1 + # filterLimits.GREGoRAF_UNA 0:1 + # filterByRange.GREGoRAF_UNK on + # filterLabel.GREGoRAF_UNK GREGoR Unknown AF + # filter.GREGoRAF_UNK 0:1 + # filterLimits.GREGoRAF_UNK 0:1 + # filterByRange.GREGoRAC_AFF on + # filterLabel.GREGoRAC_AFF GREGoR Affected AC + # filter.GREGoRAC_AFF 0:2000000 + # filterLimits.GREGoRAC_AFF 0:2000000 + # filterByRange.GREGoRAC_UNA on + # filterLabel.GREGoRAC_UNA GREGoR Unaffected AC + # filter.GREGoRAC_UNA 0:2000000 + # filterLimits.GREGoRAC_UNA 0:2000000 + # filterByRange.GREGoRAC_UNK on + # filterLabel.GREGoRAC_UNK GREGoR Unknown AC + # filter.GREGoRAC_UNK 0:2000000 + # filterLimits.GREGoRAC_UNK 0:2000000 # SCHEMA populations - filterByRange.SCHEMAAF_CASE on - filterLabel.SCHEMAAF_CASE SCHEMA Schizophrenia case AF - filterByRange.SCHEMAAF_CTRL on - filterLabel.SCHEMAAF_CTRL SCHEMA Control AF - filterByRange.SCHEMAAC_CASE on - filterLabel.SCHEMAAC_CASE SCHEMA Schizophrenia case AC - filterByRange.SCHEMAAC_CTRL on - filterLabel.SCHEMAAC_CTRL SCHEMA Control AC + # filterByRange.SCHEMAAF_CASE on + # filterLabel.SCHEMAAF_CASE SCHEMA Schizophrenia case AF + # filter.SCHEMAAF_CASE 0:1 + # filterLimits.SCHEMAAF_CASE 0:1 + # filterByRange.SCHEMAAF_CTRL on + # filterLabel.SCHEMAAF_CTRL SCHEMA Control AF + # filter.SCHEMAAF_CTRL 0:1 + # filterLimits.SCHEMAAF_CTRL 0:1 + # filterByRange.SCHEMAAC_CASE on + # filterLabel.SCHEMAAC_CASE SCHEMA Schizophrenia case AC + # filter.SCHEMAAC_CASE 0:2000000 + # filterLimits.SCHEMAAC_CASE 0:2000000 + # filterByRange.SCHEMAAC_CTRL on + # filterLabel.SCHEMAAC_CTRL SCHEMA Control AC + # filter.SCHEMAAC_CTRL 0:2000000 + # filterLimits.SCHEMAAC_CTRL 0:2000000 # WBBC China populations - filterByRange.WBBCAF_North on - filterLabel.WBBCAF_North WBBC China North Han AF - filterByRange.WBBCAF_Central on - filterLabel.WBBCAF_Central WBBC China Central Han AF - filterByRange.WBBCAF_South on - filterLabel.WBBCAF_South WBBC China South Han AF - filterByRange.WBBCAF_Lingnan on - filterLabel.WBBCAF_Lingnan WBBC China Lingnan Han AF - filterByRange.WBBCAC_North on - filterLabel.WBBCAC_North WBBC China North Han AC - filterByRange.WBBCAC_Central on - filterLabel.WBBCAC_Central WBBC China Central Han AC - filterByRange.WBBCAC_South on - filterLabel.WBBCAC_South WBBC China South Han AC - filterByRange.WBBCAC_Lingnan on - filterLabel.WBBCAC_Lingnan WBBC China Lingnan Han AC + # filterByRange.WBBCAF_North on + # filterLabel.WBBCAF_North WBBC China North Han AF + # filter.WBBCAF_North 0:1 + # filterLimits.WBBCAF_North 0:1 + # filterByRange.WBBCAF_Central on + # filterLabel.WBBCAF_Central WBBC China Central Han AF + # filter.WBBCAF_Central 0:1 + # filterLimits.WBBCAF_Central 0:1 + # filterByRange.WBBCAF_South on + # filterLabel.WBBCAF_South WBBC China South Han AF + # filter.WBBCAF_South 0:1 + # filterLimits.WBBCAF_South 0:1 + # filterByRange.WBBCAF_Lingnan on + # filterLabel.WBBCAF_Lingnan WBBC China Lingnan Han AF + # filter.WBBCAF_Lingnan 0:1 + # filterLimits.WBBCAF_Lingnan 0:1 + # filterByRange.WBBCAC_North on + # filterLabel.WBBCAC_North WBBC China North Han AC + # filter.WBBCAC_North 0:2000000 + # filterLimits.WBBCAC_North 0:2000000 + # filterByRange.WBBCAC_Central on + # filterLabel.WBBCAC_Central WBBC China Central Han AC + # filter.WBBCAC_Central 0:2000000 + # filterLimits.WBBCAC_Central 0:2000000 + # filterByRange.WBBCAC_South on + # filterLabel.WBBCAC_South WBBC China South Han AC + # filter.WBBCAC_South 0:2000000 + # filterLimits.WBBCAC_South 0:2000000 + # filterByRange.WBBCAC_Lingnan on + # filterLabel.WBBCAC_Lingnan WBBC China Lingnan Han AC + # filter.WBBCAC_Lingnan 0:2000000 + # filterLimits.WBBCAC_Lingnan 0:2000000 skipEmptyFields on track varFreqsArray shortLabel Genotyping Array Databases Combined longLabel SNV Frequencies: Genotyping-array cohorts combined (TPMI, Mexico Biobank, UK Biobank imputed) type bigBed 9 + parent varFreqs off bigDataUrl /gbdb/$D/varFreqs/_array/varFreqsArray.bb tableBrowser off visibility hide itemRgb on maxWindowToDraw 5000000 priority 0.2 mouseOver <b>Var:</b> $name<br><b>AA change:</b> $aaChange<br><b>Var type:</b> $varType<br><b>Conseq:</b> $consequence<br><b>Max AF:</b> $maxAF<br><b>Total AC:</b> $totalAC<br><b>Sources:</b> $sources filterValues.sources TPMI|TPMI Taiwan,MexBB|Mexico Biobank,UKBB|UK Biobank imputed filterType.sources multipleListOr filterLabel.sources Source Database filterValues.varType SNV|SNV,INS|Insertion,DEL|Deletion,MNV|MNV filterLabel.varType Variant Type filterValues.consequence missense|Missense,synonymous|Synonymous,stop_gained|Stop Gained,frameshift|Frameshift,splice_donor|Splice Donor,splice_acceptor|Splice Acceptor,intron|Intron,3_prime_utr|3' UTR,5_prime_utr|5' UTR,non_coding|Non-coding,.|Intergenic,others|Other filterType.consequence multipleListOr filterLabel.consequence Consequence filterByRange.refLen on filterLabel.refLen Reference Length filterByRange.altLen on filterLabel.altLen Alternate Length filterByRange.varLen on filterLabel.varLen Length Change filterByRange.maxAF on filterLabel.maxAF Max Allele Frequency filterLimits.maxAF 0:1 filterByRange.totalAC on filterLabel.totalAC Total Allele Count (all databases) filterByRange.TPMIAF on filterLabel.TPMIAF TPMI Taiwan AF filterByRange.MexBBAF on filterLabel.MexBBAF Mexico Biobank AF filterByRange.UKBBAF on filterLabel.UKBBAF UK Biobank imputed AF filterByRange.TPMIAC on filterLabel.TPMIAC TPMI Taiwan AC filterByRange.MexBBAC on filterLabel.MexBBAC Mexico Biobank AC filterByRange.UKBBAC on filterLabel.UKBBAC UK Biobank imputed AC skipEmptyFields on track allofus shortLabel AllOfUs v7 245k WGS longLabel SNV Frequencies: AllOfUs v7 - 245k WGS, local-ancestry-stratified, AC>=20 type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/_allofus/allOfUs.locAncFreq.vcf.gz dataVersion V7 visibility hide tableBrowser off priority 2 #track me #shortLabel Regeneron Million Exomes 983k WES #longLabel SNV Frequencies: Regeneron One Million Exomes (ME) Project - 983k WGS #parent varFreqs on #bigDataUrl /gbdb/$D/varFreqs/me/me.freq.vcf.gz #visibility pack #type vcfTabix #hapClusterEnabled true #dataVersion 10/04/2023, v1.1.3 #tableBrowser off #priority 1 track topmed shortLabel NHLBI TOPMed 10 151k WGS longLabel SNV Frequencies: NHLBI TOPMed - 151k WGS type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/_topmed/topmed10.vcf.gz dataVersion Freeze 10 tableBrowser off visibility hide priority 22 track sfariSparkExomes shortLabel SFARI SPARK 140k WES longLabel SNV Frequencies: SFARI SPARK - 140k WES type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/_sfari/SPARK.iWES_v3.2024_08.deepvariant.norm.vcf.gz dataVersion iWES v3 2024_08 tableBrowser off visibility hide priority 26 track sfariSparkWgs shortLabel SFARI SPARK 12k WGS longLabel SNV Frequencies: SFARI SPARK - 12,519 WGS type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/_sfari/wgs_12519_genome.deepvariant.norm.vcf.gz dataVersion iWGS v1.1 visibility hide priority 25 html sfariSparkExomes tableBrowser off #track mcps #shortLabel Mexico City Prospective Study 10k WGS+141k WES #longLabel SNV Frequencies: Mexico City Prospective Study (MCPS) #tableBrowser off #parent varFreqs on #bigDataUrl /gbdb/$D/varFreqs/mcps/mcps.freq.vcf.gz #visibility pack #type vcfTabix #dataVersion May 2023 (v1.2.0) #priority 3 track tommo60kjpn shortLabel Japan ToMMo 61k WGS longLabel SNV Frequencies: Japan 61k - ToMMo SNV+Indels type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/tommo61kjpn/tommo-61kjpn-20250616-GRCh38-snvindel-af-autosome.vcf.gz visibility hide dataVersion 2025-06-16 priority 17 track wbbc shortLabel China WBBC 4.5k WGS longLabel SNV Frequencies: Westlake BioBank for Chinese - 4,480 WGS, 4 regional Han groups type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/wbbc/wbbc.vcf.gz visibility hide dataVersion Phase I v20210103 priority 6 track chinamap shortLabel China ChinaMAP 10.5k WGS longLabel SNV Frequencies: ChinaMAP phase 1 - 10,588 WGS at ~40x, Chinese natural population type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/_chinamap/chinamap.vcf.gz visibility hide dataVersion Phase 1 (v2020-03.beta) priority 5 tableBrowser off track tpmi shortLabel Taiwan TPMI Axiom array longLabel SNV Frequencies: Taiwan Precision Medicine Initiative - Axiom TPM1 chip, Han Chinese type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/_tpmi/tpmi.vcf.gz visibility hide dataVersion Axiom TPM1 2022-06 priority 31 tableBrowser off track alfaVcf shortLabel NCBI ALFA 408k mixed longLabel SNV Frequencies: NCBI ALFA (dbGaP data) - 408k mixed WGS/WES/array, 163M variants type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/alfa/ALFA.vcf.gz visibility hide dataVersion R4 priority 20 url https://www.ncbi.nlm.nih.gov/snp/$$#frequency_tab urlLabel NCBI Variation Page track finngen parent varFreqs on visibility hide type vcfTabix shortLabel FinnGen R12 500k imputed longLabel SNV Frequencies: Finland FinnGen - 500k samples, arrays, imputation used 8.5k WGS priority 8 bigDataUrl /gbdb/$D/varFreqs/_finngen/finnge_R12_annotated_variants_v1.vcf.gz dataVersion R12 tableBrowser off track ukbb parent varFreqs on visibility hide type vcfTabix shortLabel UK Biobank 361k imputed longLabel SNV Frequencies: UK Biobank Genotypes - 361k White British, Neale Lab Round 2 imputed priority 32 bigDataUrl /gbdb/$D/varFreqs/ukbb/ukbb.vcf.gz dataVersion Neale Lab R2 08-2018 track swefreq parent varFreqs on visibility hide type vcfTabix shortLabel Sweden SweGen 1k WGS longLabel SNV Frequencies: Sweden SweGen - 1k WGS priority 30 bigDataUrl /gbdb/$D/varFreqs/_swefreq/swegen_frequencies_fixploidy_GRCh38_20190204.vcf.gz dataVersion 20251201 tableBrowser off track gonl parent varFreqs on visibility hide type vcfTabix shortLabel Netherlands GoNL 498 WGS longLabel SNV Frequencies: Genome of the Netherlands - 250 Dutch trios priority 21 bigDataUrl /gbdb/$D/varFreqs/gonl/gonl.vcf.gz dataVersion GRCh38 1.0 track mgrb shortLabel Australia MGRB 4k WGS longLabel SNV Frequencies: Australia Medical Genome Reference Bank - 4,011 WGS type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/_mgrb/MGRB.phase3.GRCh38.norm.vcf.gz dataVersion Phase 3 visibility hide priority 3 # no downloads as per Matt Hobbs email Jan 28 2026 tableBrowser off track gasp shortLabel GenomeAsia 1.7k SNVs longLabel SNV Frequencies: GenomeAsia Pilot - Substitutions type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/ga100k/ga100k.subst.vcf.gz visibility hide priority 11 dataVersion Pilot 2019 (lifted to hg38, May 2026) track gaspIndel shortLabel GenomeAsia 1.7k Indels longLabel SNV Frequencies: GenomeAsia Pilot - Indels type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/ga100k/ga100k.indels.vcf.gz visibility hide priority 10 dataVersion Pilot 2019 (lifted to hg38, May 2026) html gasp track abraom shortLabel Brazil ABraOM 1k WGS longLabel SNV Frequencies: ABraOM Brazil - 1,171 unrelated individuals type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/abraom/abraom.vcf.gz visibility hide priority 4 dataVersion SABE-WGS-1171 Sep 2020 track indigenomes shortLabel India IndiGenomes 1k WGS longLabel SNV Frequencies: IndiGenomes India - 1,029 samples type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/indigenomes/IndiGenomes_Variants.vcf.gz visibility hide priority 16 dataVersion IndiGen pilot (Jain 2021) track genomeindia shortLabel India GenomeIndia 9.7k WGS longLabel SNV Frequencies: GenomeIndia - 9,768 WGS, 83 populations (Bhattacharyya 2025) type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/_genomeindia/genomeindia.vcf.gz tableBrowser off visibility hide dataVersion 9768GI_SummaryStats (Apr 2025) priority 15 track kova shortLabel Korea KOVA 5.3k mixed longLabel SNV Frequencies: KOVA Korea - 5305 samples, 1.9k WGS+3.4k WES type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/_kova/kova.v7.vcf.gz visibility hide priority 18 tableBrowser off dataVersion V7 track npm shortLabel Singapore NPM 9.7k WGS longLabel SNV Frequencies: NPM Singapore - 9,770 WGS samples type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/_npm/SG10K_Health_r5.3.2.sites.vcf.bgz visibility hide priority 28 tableBrowser off dataVersion r5.3.2 track hrc shortLabel HRC 30k WGS longLabel SNV Frequencies: Haplotype Reference Consortium - 30k WGS (excl. 1000 Genomes) type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/hrc/hrc.vcf.gz visibility hide priority 14 dataVersion r1.1 track saudi shortLabel Saudi Genome 302 WGS longLabel SNV Frequencies: Saudi Genome Project - 302 WGS samples type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/saudi/saudi.vcf.gz visibility hide priority 23 dataVersion SHGP (figshare 51297884, 2025) track schema shortLabel SCHEMA 121k WES Sz longLabel SNV Frequencies: SCHEMA Schizophrenia Exome Meta-Analysis - WES 24k cases, 97k controls type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/schema/SCHEMA_variant_results_withAF.vcf.gz visibility hide dataVersion 2022 priority 24 url https://schema.broadinstitute.org/ urlLabel SCHEMA Browser track mxbFreq shortLabel Mexico Biobank 6k Array longLabel SNV Frequencies: Mexico Biobank - 6,011 individuals, genotyping array type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/_mxb/mxb.freq.vcf.gz visibility hide dataVersion Nov 2025 (hg38 lift) tableBrowser off priority 19 track sgdpFreq shortLabel SGDP 279 WGS longLabel SNV Frequencies: Simons Genome Diversity Project - 279 WGS, 142 populations type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/sgdpFreq/sgdp.freq.vcf.gz visibility hide dataVersion 2016-12-07 (hg38 lift) priority 27 track gregor shortLabel GREGoR R4 3.6k WGS longLabel SNV Frequencies: GREGoR Consortium - Release 4, 3,624 WGS samples, rare disease families type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/gregor/gregor.vcf.gz visibility hide dataVersion R04 (Oct 2025) priority 13 track hgdp1kFreq shortLabel gnomAD HGDP+1kG 4k WGS longLabel SNV Frequencies: gnomAD HGDP + 1000 Genomes - 4,094 WGS, 80 populations type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/hgdp1kFreq/hgdp1k.freq.vcf.gz visibility hide dataVersion v3.1.2 priority 12 track ga4kSnv shortLabel GA4K 552 PacBio LR longLabel SNV Frequencies: GA4K Children's Mercy - 552 PacBio HiFi WGS, pediatric RD type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/ga4k/ga4kSnv.vcf.gz visibility hide dataVersion Cohen 2022 release priority 9 track colorsDbSnv shortLabel CoLoRSdb 1k LR SNV/Ind longLabel SNV Frequencies: CoLoRSdb v1.2.0 - 1,027 PacBio HiFi WGS, SNV/indel callset type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/colorsDb/colorsDbSnv.vcf.gz visibility hide dataVersion v1.2.0 priority 7 track svatalogSnv shortLabel SVatalog 101 WGS longLabel SNV Frequencies: GWAS SVatalog - 101 samples, 10X Genomics linked-read SNPs type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/svatalog/svatalog.vcf.gz visibility hide dataVersion Chirmade 2025 release priority 29 track tishkoff180 shortLabel 12 Afr Pops 180 WGS longLabel SNV Frequencies: 180 WGS from 12 Indigenous African Populations (Fan 2023) type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/_tishkoff/tishkoff180.vcf.gz visibility hide dataVersion Cell 2023 (hg19 lift) tableBrowser off priority 1