src/hg/makeDb/doc/hg19.txt 1.87

Index: src/hg/makeDb/doc/hg19.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/hg19.txt,v
retrieving revision 1.86
retrieving revision 1.87
diff -b -B -U 4 -r1.86 -r1.87
--- src/hg/makeDb/doc/hg19.txt	25 Feb 2010 23:47:50 -0000	1.86
+++ src/hg/makeDb/doc/hg19.txt	1 Mar 2010 21:05:26 -0000	1.87
@@ -8335,22 +8335,26 @@
     featureBits hg19 vegaPseudoGene
     # 6885145 bases of 2897316137 (0.238%) in intersection
 
 ########################################################################
-# NHGRI GWAS CATALOG (DONE 1/19/10 angie)
+# NHGRI GWAS CATALOG (DONE 3/1/10 angie)
+# Originally done 1/19/10
     mkdir /hive/data/genomes/hg19/bed/gwasCatalog
     cd /hive/data/genomes/hg19/bed/gwasCatalog
-
-    # Mapping to hg19 by joining hg19 SNP coords with catalog flatfile (see hg18.txt)
     cut -f 1-4 ../snp130/snp130.bed \
     | sort -k4,4 \
-    | join -t "^V       " -1 4 - /hive/data/genomes/hg18/bed/gwasCatalog/noCoords.100115.tab \
+      > snp130Coords.bed
+    mkdir /hive/data/genomes/hg19/bed/gwasCatalog/100301
+    cd /hive/data/genomes/hg19/bed/gwasCatalog/100301
+
+    # Mapping to hg19 by joining hg19 SNP coords with catalog flatfile (see hg18.txt)
+    join -t "	" -1 4 ../snp130Coords.bed /hive/data/genomes/hg18/bed/gwasCatalog/100301/noCoords.tab \
         -o 1.1,1.2,1.3,1.4,2.2,2.3,2.4,2.5,2.6,2.7,2.8,2.9,2.10,2.11,2.12,2.13,2.14,2.15,2.16,2.17,2.18,2.19 \
     | sort -k1,1 -k2n,2n \
         > gwasCatalog.bed
-
     hgLoadBed hg19 gwasCatalog gwasCatalog.bed \
       -tab -sqlTable=$HOME/kent/src/hg/lib/gwasCatalog.sql -notItemRgb -allowStartEqualEnd
+#Loaded 2780 elements of size 22
 
 
 ######################################################################## 
 # ailMel1 Panda alignment (DONE - 2010-02-04 - Hiram)