442e433a90b25deb87f10e6cf1b7b608bb0a6d67 max Sat Sep 26 21:56:06 2026 -0700 sfariSparkWgs45kAsd: flag 25M insertions of non-human (oral bacteria) sequence as FILTER NonHumanIns and hide them by default; add SFARI SPARK 45k WGS to the combined tracks without those insertions and relabel the 12k pilot as SFARI SPARK iWGS v1.1 Pilot, refs #38424 diff --git src/hg/makeDb/scripts/varFreqs/populations.tsv src/hg/makeDb/scripts/varFreqs/populations.tsv index 6c8bfd17b01..b6c8f9a8c84 100644 --- src/hg/makeDb/scripts/varFreqs/populations.tsv +++ src/hg/makeDb/scripts/varFreqs/populations.tsv @@ -3,30 +3,32 @@ # Optional 6th column "phenotype" (affected|unaffected|unknown) tags a disease cohort's # case/control arms so the build can aggregate an affected-vs-unaffected summary across # cohorts. Ancestry/region populations leave it blank. # 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 # SFARI SPARK autism phenotype split (asd column of individuals_registration) SPARK AUT ASD proband AC_AUT AF_AUT affected SPARK NON_AUT Non-ASD family AC_NON_AUT AF_NON_AUT unaffected SFARI_WGS AUT ASD proband AC_AUT AF_AUT affected SFARI_WGS NON_AUT Non-ASD family AC_NON_AUT AF_NON_AUT unaffected +SPARK45k AUT ASD proband AC_AUT AF_AUT affected +SPARK45k NON_AUT Non-ASD family AC_NON_AUT AF_NON_AUT unaffected # SCHEMA schizophrenia case/control split (summed across analysis groups) SCHEMA CASE Schizophrenia case AC_CASE AF_CASE affected SCHEMA CTRL Control AC_CTRL AF_CTRL unaffected # 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