src/hg/makeDb/doc/hg18.txt 1.355

Index: src/hg/makeDb/doc/hg18.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/hg18.txt,v
retrieving revision 1.354
retrieving revision 1.355
diff -b -B -U 4 -r1.354 -r1.355
--- src/hg/makeDb/doc/hg18.txt	11 Mar 2009 17:59:09 -0000	1.354
+++ src/hg/makeDb/doc/hg18.txt	11 Mar 2009 18:31:44 -0000	1.355
@@ -21253,21 +21253,22 @@
     hgLoadGenePred -genePredExt hg18 vegaPseudoGene pseudo.gp
 
 
 ############################################################################
-# DGV V6 (DATABASE OF GENOMIC VARIANTS) (DONE 2/23/09 angie)
+# DGV V7 (DATABASE OF GENOMIC VARIANTS) (DONE 3/11/09 angie)
+# DGV V6 thin regions dropped 2/23/09
 # DGV V6 with useless thin regions done 11/12/08
 # DGV V5 done 7/16/08
 # DGV V4 done 5/9/08
     ssh hgwdev
-    mkdir /cluster/data/hg18/bed/dgv.v6
-    cd /cluster/data/hg18/bed/dgv.v6
+    mkdir /hive/data/genomes/hg18/bed/dgv.v7
+    cd /hive/data/genomes/hg18/bed/dgv.v7
     wget --timestamping \
-      http://projects.tcag.ca/variation/downloads/variation.hg18.v6.nov.2008.txt
+      http://projects.tcag.ca/variation/downloads/variation.hg18.v7.mar.2009.txt
     wget --timestamping \
-      http://projects.tcag.ca/variation/downloads/indel.hg18.v6.nov.2008.txt
+      http://projects.tcag.ca/variation/downloads/indel.hg18.v7.mar.2009.txt
     # shuffle fields into bed8+
-    foreach f (*.v6.*.txt)
+    foreach f (*.v7.*.txt)
       tail -n +2 $f \
       | perl -wpe 'chomp; \
         ($id, $landmark, $chr, $start, $end, $varType, \
          undef, undef, undef, $ref, $pmid, $method, \
@@ -21282,12 +21283,14 @@
                   $start, $end, $rgb, $landmark, $varType, \
                   $ref, $pmid, $method, $sample) . "\n";' \
           > $f:r.bed
     end
-    hgsql hg18 -e 'rename table dgv to dgvV5'
+    hgsql hg18 -e 'rename table dgv to dgvV6'
     hgLoadBed hg18 dgv *.bed \
       -onServer -sqlTable=$HOME/kent/src/hg/lib/dgv.sql -tab
-#Loaded 31615 elements of size 15
+#Loaded 38406 elements of size 15
+      hgsql hg18 -NBe 'select count(distinct(pubMedId)) from dgv;'
+#31
 
 
 ############################################################################
 # AGILENT CGH PROBES (AND MM8, RN4) (Done 2008-05-13, Andy)