c7b6da0a433f53fdf3c4137a67598d099d9ce1a5
max
  Wed Jan 14 10:52:53 2026 -0800
adding SFARI SPARK to varFreqs supertrack, refs #36642

diff --git src/hg/makeDb/doc/hg38/varFreqs.txt src/hg/makeDb/doc/hg38/varFreqs.txt
index 9d8d734bfcf..31d7caf0c41 100644
--- src/hg/makeDb/doc/hg38/varFreqs.txt
+++ src/hg/makeDb/doc/hg38/varFreqs.txt
@@ -68,15 +68,28 @@
 tabix -p vcf kova.v7.vcf.gz
 
 # NPM Singapore
 cd /hive/data/genomes/hg38/bed/varFreqs/npm/
 # downloaded data manually from chorus website, https://chorus.grids-platform.io/vcfdl
 bcftools concat  --threads 10  -Oz -o SG10K_Health_r5.3.2.sites.vcf.bgz  SG10K_Health_r5.3.2.sites.chr{1..22}.vcf.bgz SG10K_Health_r5.3.2.sites.chrX.vcf.bgz SG10K_Health_r5.3.2.sites.chrY.vcf.bgz 
 tabiv -p vcf SG10K_Health_r5.3.2.sites.vcf.bgz
 
 # Saudi 300 genomes
 cd /hive/data/genomes/hg38/bed/varFreqs/saudi
 wget https://figshare.com/ndownloader/files/51297884 -O 51297884.tsv.gz
 python3 ~/kent/src/hg/makeDb/scripts/saudiToVcf.py
 bgzip saudi.vcf
 tabix -p vcf saudi.vcf.gz
 
+# SFARI SPARK
+cd /hive/data/genomes/hg38/bed/varFreqs/sparkExomes/
+# used globus to download into vcf/
+sh ~/kent/src/hg/makeDb/scripts/sparkMergeVcfAddCounts.sh vcf/SPARK.iWES_v3.2024_08.deepvariant 8
+bcftools norm -m-  SPARK.iWES_v3.2024_08.deepvariant.sites.vcf.gz -Oz > SPARK.iWES_v3.2024_08.deepvariant.norm.vcf.gz && tabix -p vcf SPARK.iWES_v3.2024_08.deepvariant.norm.vcf.gz
+
+cd /hive/data/genomes/hg38/bed/varFreqs/sparkWgs/
+# used globus to download into vcf/
+sh ~/kent/src/hg/makeDb/scripts/sparkMergeVcfAddCounts.sh vcf/wgs_12519_genome.deepvariant 8 
+bcftools norm -m-  wgs_12519_genome.deepvariant.sites.vcf.gz -Oz > wgs_12519_genome.deepvariant.norm.vcf.gz
+tabix -p vcf wgs_12519_genome.deepvariant.norm.vcf.gz
+
+