8102c8c2b15180f3e48534af65f117ac467c4505
jcasper
  Thu Apr 14 16:00:15 2022 -0700
Makedoc for initial DECIPHER build on hg38, refs #29130

diff --git src/hg/makeDb/doc/hg38/hg38.txt src/hg/makeDb/doc/hg38/hg38.txt
index 5ad8e9b..7624f37 100644
--- src/hg/makeDb/doc/hg38/hg38.txt
+++ src/hg/makeDb/doc/hg38/hg38.txt
@@ -6997,15 +6997,39 @@
 #Downloaded by web browser
 cd /hive/data/genomes/hg38/bed/agilentProbes/genetiSureCyto
 fetchChromSizes hg38 > hg38.chrom.sizes
 bedSort hg38.GenetiSure_Cyto_CGH+SNP_Microarray_4x180K_085591_D_BED_20200302.bed hg38.GenetiSure_Cyto_CGH+SNP_Microarray_4x180K_085591_D_BED_20200302.bed
 bedToBigBed hg38.GenetiSure_Cyto_CGH+SNP_Microarray_4x180K_085591_D_BED_20200302.bed hg38.chrom.sizes hg38.GenetiSure_Cyto_CGH+SNP_Microarray_4x180K_085591_D_BED_20200302.bb
 bedSort hg38.GenetiSure_Cyto_CGH_Microarray_8x60K_085590_D_BED_20200302.bed hg38.GenetiSure_Cyto_CGH_Microarray_8x60K_085590_D_BED_20200302.bed
 bedToBigBed hg38.GenetiSure_Cyto_CGH_Microarray_8x60K_085590_D_BED_20200302.bed hg38.chrom.sizes hg38.GenetiSure_Cyto_CGH_Microarray_8x60K_085590_D_BED_20200302.bb
 bedSort hg38.GenetiSure_Cyto_CGH_Microarray_4x180K_085589_D_BED_20200302.bed hg38.GenetiSure_Cyto_CGH_Microarray_4x180K_085589_D_BED_20200302.bed
 bedToBigBed hg38.GenetiSure_Cyto_CGH_Microarray_4x180K_085589_D_BED_20200302.bed hg38.chrom.sizes hg38.GenetiSure_Cyto_CGH_Microarray_4x180K_085589_D_BED_20200302.bb
 mkdir -p /gbdb/hg38/snpCnvArrays/agilent
 cd /gbdb/hg38/snpCnvArrays/agilent
 ln -s /hive/data/genomes/hg38/bed/agilentProbes/genetiSureCyto/hg38.GenetiSure_Cyto_CGH+SNP_Microarray_4x180K_085591_D_BED_20200302.bb
 ln -s /hive/data/genomes/hg38/bed/agilentProbes/genetiSureCyto/hg38.GenetiSure_Cyto_CGH_Microarray_8x60K_085590_D_BED_20200302.bb
 ln -s /hive/data/genomes/hg38/bed/agilentProbes/genetiSureCyto/hg38.GenetiSure_Cyto_CGH_Microarray_4x180K_085589_D_BED_20200302.bb
 vi ~/kent/src/hg/makeDb/trackDb/human/hg38/trackDb.ra
+
+#########################################################################
+# DECIPHER CNV & SNV - initial build (DONE 2022-04-08 Jonathan)
+# RM 29130
+
+cd /hive/data/genomes/outside/otto/decipher
+mkdir 2022-04-05
+cd 2022-04-05
+
+# manually fetch decipher-variants-grch38-2022-04-03.bed from DECIPHER
+../buildDecipher decipher-variants-grch38-2022-04-03.bed
+
+for i in `cat ../decipher.tables`
+        do
+        n=$i"New"
+        o=$i"Old"
+        hgsqlSwapTables hg38 $n $i $o -dropTable3
+        done
+
+mkdir -p /gbdb/hg38/decipher
+cd /gbdb/hg38/decipher
+ln -s /hive/data/outside/otto/decipher/2022-04-05/decipherCnv.bb .
+
+#########################################################################