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