2e2155ca3de501f17408b1cb11ff074a3ccb4b2c
kate
  Tue Nov 5 12:03:43 2019 -0800
Add gnomAD variants for hg38. refs #21782

diff --git src/hg/makeDb/doc/hg38/gnomad.txt src/hg/makeDb/doc/hg38/gnomad.txt
index f2f461b..4dfaa2c 100644
--- src/hg/makeDb/doc/hg38/gnomad.txt
+++ src/hg/makeDb/doc/hg38/gnomad.txt
@@ -47,15 +47,42 @@
 # 743.06 GiB, MD5: 83de3d5b52669f714e810d4fcf047c18
 wget https://storage.googleapis.com/gnomad-public/release/2.1.1/liftover_grch38/vcf/genomes/gnomad.genomes.r2.1.1.sites.liftover_grch38.vcf.bgz >&! wget.genomes.log &
 
 # from log:  3 hrs download time
 #--2019-10-07 17:03:11--  https://storage.googleapis.com/gnomad-public/release/2.1.1/liftover_grch38/vcf/genomes/gnomad.genomes.r2.1.1.sites.liftover_grch38.vcf.bgz
 # 2019-10-07 20:02:56 (70.6 MB/s) - 'gnomad.genomes.r2.1.1.sites.liftover_grch38.vcf.bgz' saved [797851733355/797851733355]
 
 ln -s `pwd`/gnomad.genomes.r2.1.1.sites.liftover_grch38.vcf.bgz /gbdb/hg38/gnomAD/vcf/gnomad.genomes.r2.1.1.sites.liftover_grch38.vcf.gz
 
 wget https://storage.googleapis.com/gnomad-public/release/2.1.1/liftover_grch38/vcf/genomes/gnomad.genomes.r2.1.1.sites.liftover_grch38.vcf.bgz.tbi
 ln -s `pwd`/gnomad.genomes.r2.1.1.sites.liftover_grch38.vcf.bgz.tbi /gbdb/hg38/gnomAD/vcf/gnomad.genomes.r2.1.1.sites.liftover_grch38.vcf.gz.tbi
 
 #################
 Use/adapt trackDb and HTML from hg19 track
 
+#################
+# Add V3.  Native hg38 analysis (not lifted)
+# Released 10/16/2019 by MacArthur lab, announced here:
+# https://macarthurlab.org/2019/10/16/gnomad-v3-0/
+# (2019-10-21 kate)
+
+mkdir /hive/data/outside/gnomAD.3
+cd /hive/data/outside/gnomAD.3
+
+wget https://storage.googleapis.com/gnomad-public/release/3.0/vcf/genomes/gnomad.genomes.r3.0.sites.vcf.bgz.tbi
+
+ln -s `pwd`/gnomad.genomes.r3.0.sites.vcf.bgz.tbi /gbdb/hg38/gnomAD/vcf/gnomad.genomes.r3.0.sites.vcf.gz.tbi
+
+(date; wget https://storage.googleapis.com/gnomad-public/release/3.0/vcf/genomes/gnomad.genomes.r3.0.sites.vcf.bgz; date) >&! wget.genomes.log &
+
+#Mon Oct 21 11:26:58 PDT 2019
+#Mon Oct 21 12:27:14 PDT 2019
+#    ~1 hr
+
+md5sum gnomad.genomes.r3.0.sites.vcf.bgz
+
+ln -s `pwd`/gnomad.genomes.r3.0.sites.vcf.bgz /gbdb/hg38/gnomAD/vcf/gnomad.genomes.r3.0.sites.vcf.gz
+
+
+
+
+