ca3f7e9e7bebb3ea6f35844fc03c90a988eb1330
angie
  Fri Oct 18 15:02:51 2019 -0700
bigDbSnp: add Common, ClinVar, Mult subset tracks to bigBed and install steps.  refs #23283

diff --git src/hg/makeDb/doc/bigDbSnp.txt src/hg/makeDb/doc/bigDbSnp.txt
index 8fca709..5b27f29 100644
--- src/hg/makeDb/doc/bigDbSnp.txt
+++ src/hg/makeDb/doc/bigDbSnp.txt
@@ -180,30 +180,35 @@
 # 13027110 commonAll
 # 19258751 commonSome
 #   836327 diffMajor
 #     7736 freqIsAmbiguous
 #    36306 freqNotRefAlt
 #   130175 multiMap
 #102260850 overlapDiffClass
 # 15075710 overlapSameClass
 #      110 refIsAmbiguous
 #  3033691 refIsMinor
 #   189809 refIsRare
 #    63804 refIsSingleton
 #       33 refMismatch
 #  4439534 revStrand
 
+    # 10/18/19: add subset tracks
+    $HOME/kent/src/hg/utils/automation/doBigDbSnp.pl $topDir 152 $freqSourceOrder \
+       -buildDir=`pwd` -continue=bigBed -stop=install >& subsets.log &
+    tail -f subsets.log
+
 
 ##############################################################################
 # dbSnp153: dbSNP build 153 (DONE 9/19/19 angie)
 
     topDir=/hive/data/outside/dbSNP/153
     mkdir -p $topDir/json
     cd $topDir/json
     wget --timestamping -nd ftp://ftp.ncbi.nih.gov/snp/latest_release/JSON/\*
     md5sum -c CHECKSUMS
 #refsnp-chr10.json.bz2: OK
 #...
 #refsnp-withdrawn.json.bz2: OK
 
     # jsonQuery commands to figure out what assemblies, SO terms and frequency sources are in there,
     # by sampling first 10,000 variants on an arbitrary chrom:
@@ -395,17 +400,24 @@
 # 12430253 commonAll
 # 20893174 commonSome
 #  3573503 diffMajor
 #     7749 freqIsAmbiguous
 #    39038 freqNotRefAlt
 #   132015 multiMap
 #109838613 overlapDiffClass
 # 17228657 overlapSameClass
 #      111 refIsAmbiguous
 # 16277729 refIsMinor
 #   166192 refIsRare
 #    56491 refIsSingleton
 #       33 refMismatch
 #  4512600 revStrand
 
+    # 10/18/19: add subset tracks
+    # I added new commands to the bigBed and install steps of doBigDbSnp.pl,
+    # ran -debug and copy-pasted commands from the generated scripts.
+    $HOME/kent/src/hg/utils/automation/doBigDbSnp.pl $topDir 152 $freqSourceOrder \
+       -buildDir=`pwd` -continue=bigBed -stop=install \
+       -debug
+
 
 ##############################################################################