ef63626263c7b8d43c6820ff158490f4e0d8a616
max
  Tue Nov 25 08:59:03 2025 -0800
adding track docs to previous commit

diff --git src/hg/makeDb/doc/hg38/varFreqs.txt src/hg/makeDb/doc/hg38/varFreqs.txt
index 1ab1f46a6f2..151ce2b6182 100644
--- src/hg/makeDb/doc/hg38/varFreqs.txt
+++ src/hg/makeDb/doc/hg38/varFreqs.txt
@@ -55,15 +55,20 @@
 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