src/hg/makeDb/doc/hg19.txt 1.72

1.72 2010/01/21 21:46:59 angie
Adding gwasCatalog (NHGRI's Catalog of Published Genome-Wide Association Studies).
Index: src/hg/makeDb/doc/hg19.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/hg19.txt,v
retrieving revision 1.71
retrieving revision 1.72
diff -b -B -U 4 -r1.71 -r1.72
--- src/hg/makeDb/doc/hg19.txt	15 Jan 2010 23:49:38 -0000	1.71
+++ src/hg/makeDb/doc/hg19.txt	21 Jan 2010 21:46:59 -0000	1.72
@@ -8308,5 +8308,23 @@
     featureBits hg19 vegaGene
     # 64888909 bases of 2897316137 (2.240%) in intersection
     featureBits hg19 vegaPseudoGene
     # 6885145 bases of 2897316137 (0.238%) in intersection
+
+########################################################################
+# NHGRI GWAS CATALOG (DONE 1/19/10 angie)
+    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 \
+        -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
+
+
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