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 . + +#########################################################################