676b58d841804f049f720cc9ba3fddec216dae61
max
  Tue Dec 2 06:22:46 2025 -0800
adding saudi arabia to variant frequencies track

diff --git src/hg/makeDb/doc/hg38/varFreqs.txt src/hg/makeDb/doc/hg38/varFreqs.txt
index 151ce2b6182..9d8d734bfcf 100644
--- src/hg/makeDb/doc/hg38/varFreqs.txt
+++ src/hg/makeDb/doc/hg38/varFreqs.txt
@@ -60,15 +60,23 @@
 tabix -p vcf SGDP.nh2.vcf.gz
 
 # KOVA
 cd /hive/data/genomes/hg38/bed/varFreqs/sgp/
 # got tsv file via google drive link from 장인수 <insoo078@kribb.re.kr> 
 # VCF converter, written by Claude Opus 4.1 using 2 lines of example input
 python ~/kent/src/hg/makeDb/scripts/kovaToVcf.py 1_KOVA.v7.tsv.gz kova.v7.vcf
 bgzip kova.v7.vcf
 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
+