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
@@ -1,74 +1,82 @@
 # Mexico Biobank, Max, Nov 8 2025
 CrossMap.py vcf /gbdb/hg19/liftOver/hg19ToHg38.over.chain.gz /hive
 /data/genomes/hg19/bed/varFreqs/mexbb/MXBv2.vcf.gz /hive/data/genomes/hg38/p14Clean/hg38.p14.fa MXBv2.lift.hg19ToHg38.vcf && bgzip MXBv2.lift.hg19ToHg38.vcf && bcftools sort MXBv2.lift.hg19ToHg38.vcf -Oz -m 200G -T /data/tmp/ -o MXBv2.lift.hg19ToHg38.vcf.gz && tabix -p vcf MXBv2.lift.hg19ToHg38.vcf.gz
 
 # Mexico City Prospective study, Max Oct 28 2025
 cd /hive/data/genomes/hg38/bed/varFreqs/mcps/
 for i in `seq 1 22` X; do wget https://rgc-mcps.regeneron.com/downloads/20230130/chr$i.freq.vcf.gz; done
 for i in `seq 1 22` X; do wget https://rgc-mcps.regeneron.com/downloads/20230130/chr$i.freq.vcf.gz.tbi; done
 mv *vcf* vcf/
 bcftools concat  --threads 16  -Oz -o mcps.freq.vcf.gz vcf/chr{1..22}.freq.vcf.gz vcf/chrX.freq.vcf.gz
 # make normal AC and AF and AN fields for mouseovers
 zcat mcps.freq.vcf.gz | sed -e 's/_RAW//g' > mcps.fix.freq.vcf
 mv -f mcps.fix.freq.vcf mcps.freq.vcf
 bgzip mcps.freq.vcf
 tabix -p vcf mcps.freq.vcf.gz 
 
 # Regeneron million exomes, Max, Nov 3 2025
 cd /hive/data/genomes/hg38/bed/varFreqs/me
 for i in `seq 1 22` X Y; do wget https://rgc-research.regeneron.com/me/downloads/20231004/rgc_me_variant_frequencies_chr${i}_20231004.vcf.gz.tbi; done
 bcftools concat  --threads 10  -Oz -o rgc_me_freqs_20231004.vcf.gz rgc_me_variant_frequencies_chr{1..22}_20231004.vcf.gz  rgc_me_variant_frequencies_chrX_20231004.vcf.gz rgc_me_variant_frequencies_chrY_20231004.vcf.gz 
 zcat rgc_me_freqs_20231004.vcf.gz | sed -e 's/ALL_//g' > rgc_me_freqs_20231004.fix.vcf
 tabix -p vcf rgc_me_freqs_20231004.vcf.gz
 
 # GA south asia 100k pilot
 cd /hive/data/genomes/hg38/bed/varFreqs/ga100k/
 parallel -j 8 wget -q --no-check-certificate https://browser.genomeasia100k.org/service/web/download_files/{}.substitutions.annot.cont_withmaf.vcf.gz ::: {1..22} X Y
 # fix the header line, remove "FORMAT"
 for i in *.vcf.gz; do echo "zcat $i |   awk 'BEGIN{OFS=\"\\t\"} /^#CHROM/{NF=8; print; next} /^#/ {print; next} {NF=8; print}' |   bgzip -c > fixed/$i" >> cmds.txt; done
 parallel -j 8 < cmds.txt
 bcftools concat  --threads 16  -Oz -o ../ga100k.subst.vcf.gz fixed/{1..22}.substitutions.annot.cont_withmaf.vcf.gz
 # add indels
 wget -q --no-check-certificate https://browser.genomeasia100k.org/service/web/download_files/All.indels.annot.cont_withmaf.vcf.gz
 # index
 tabix -p vcf ../ga100k*.vcf.gz
 tabix -p vcf All*.vcf.gz
 
 # TOPMED Freeze 10
 cd /hive/data/genomes/hg38/bed/varFreqs/topmed/
 # need to download the VCFs manually, 22 VCFs, with one time links from https://bravo.sph.umich.edu/vcfs.html
 # grrrr...
 bcftools concat  --threads 10  -Oz -o topmed10.vcf.gz {1..22}.vcf.gz X.vcf.gz 
 tabix -p vcf topmed10.vcf.gz
 
 # Abraom brazil
 # get unique download link from https://abraom.ib.usp.br/download/index.php
 cd /hive/data/genomes/hg38/bed/varFreqs/abraom/
 wget 'https://abraom.ib.usp.br/download/download-files.php?fid=RklEMTIzNDU2&key=1762266466-key690a0d62348de0.22872232' -O abraom.tar
 tar xvfz abraom.tar
 ln -s  /hive/data/genomes/hg38/p14Clean/hg38.p14.fa
 samtools faidx hg38.p14.fa 
 python ~/kent/src/hg/makeDb/scripts/abraomToVcf.py SABE1171.Abraom.clean.tsv abraom.vcf hg38.p14.fa
 tabix -p vcf abraom.vcf.gz 
 
 # SGDP
 cd /hive/data/genomes/hg38/bed/varFreqs/sgp/
 CrossMap.py vcf /gbdb/hg19/liftOver/hg19ToHg38.over.chain.gz /hive/data/genomes/hg19/bed/varFreqs/sgdp/SGDP.nh2.vcf.gz hg38.p14.fa sgdp.hg38.nh2.vcf
 bgzip sgdp.hg38.nh2.vcf
 bcftools sort sgdp.hg38.nh2.vcf.gz -Oz -m 200G -T /data/tmp/ -o sgdp.hg38.nh2.sort.vcf.gz 
 mv sgdp.hg38.nh2.sort.vcf.gz SGDP.nh2.vcf.gz
 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
+