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
@@ -1,61 +1,88 @@
 # gnomaAD for hg38
 # RM 21782
 
 # Genome Aggregation Database at the Broad
 # https://gnomad.broadinstitute.org
 
 # (2019-10-07 kate)
 
 # March 6, 2019: gnomAD 2.1.1
 
 mkdir vcf; cd vcf
 
 # hg38
 
 mkdir hg38; cd hg38
 mkdir -p /gbdb/hg38/gnomAD/vcf
 
 # Download from GRCh38 liftover section of downloads page:
 https://gnomad.broadinstitute.org/downloads#variants-grch38-liftover
 
 wget https://storage.googleapis.com/gnomad-public/release/2.1.1/README.txt
 
 # Exome variants
 
 # vcf
 # 85.31 GiB, MD5: cff8d0cfed50adc9211d1feaed2d4ca7
 wget https://storage.googleapis.com/gnomad-public/release/2.1.1/liftover_grch38/vcf/exomes/gnomad.exomes.r2.1.1.sites.liftover_grch38.vcf.bgz >&! wget.exomes.log &
 
 # from log: 20 minutes download time
 # --2019-10-07 16:40:48--  https://storage.googleapis.com/gnomad-public/release/2.1.1/liftover_grch38/vcf/exomes/gnomad.exomes.r2.1.1.sites.liftover_grch38.vcf.bgz
 # 2019-10-07 17:00:52 (72.6 MB/s) - 'gnomad.exomes.r2.1.1.sites.liftover_grch38.vcf.bgz' saved [91604348731/91604348731]
 
 du -sh *.bgz
 # 171G    gnomad.exomes.r2.1.1.sites.liftover_grch38.vcf.bgz
 
 md5sum gnomad.exomes.r2.1.1.sites.liftover_grch38.vcf.bgz
 # cff8d0cfed50adc9211d1feaed2d4ca7  gnomad.exomes.r2.1.1.sites.liftover_grch38.vcf.bgz
 
 ln -s `pwd`/gnomad.exomes.r2.1.1.sites.liftover_grch38.vcf.bgz /gbdb/hg38/gnomAD/vcf/gnomad.exomes.r2.1.1.sites.liftover_grch38.vcf.gz
 
 # index file
 wget https://storage.googleapis.com/gnomad-public/release/2.1.1/liftover_grch38/vcf/exomes/gnomad.exomes.r2.1.1.sites.liftover_grch38.vcf.bgz.tbi
 
 ln -s `pwd`/gnomad.exomes.r2.1.1.sites.liftover_grch38.vcf.bgz.tbi /gbdb/hg38/gnomAD/vcf/gnomad.exomes.r2.1.1.sites.liftover_grch38.vcf.gz.tbi
 
 # Genomes Variants
 # 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
+
+
+
+
+