80b6325af1a7076f71c1a9413d99a1784d2a7fbd dschmelt Thu May 26 17:16:48 2022 -0700 Uniq'd bed files refs #23591 diff --git src/hg/makeDb/doc/hg38/hg38.txt src/hg/makeDb/doc/hg38/hg38.txt index 7624f37..5a38b61 100644 --- src/hg/makeDb/doc/hg38/hg38.txt +++ src/hg/makeDb/doc/hg38/hg38.txt @@ -6986,35 +6986,38 @@ ln -s /hive/data/genomes/hg38/bed/panelApp/CNVregions.bb cd ~/kent/src/hg/makeDb/trackDb/human/hg38 wget https://hgwdev.gi.ucsc.edu/~bnguy/panel/hg38/panelapp.html mv panelapp.html panelApp.html curl https://hgwdev.gi.ucsc.edu/~bnguy/panel/hg38/trackDb.txt >> trackDb.ra vi trackDb.ra cd ~/kent/src/hg/makeDb/trackDb make alpha DBS=hg38 ###### #Agilent SNP/CNV arrays 3/11/21 #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 +uniq hg38.GenetiSure_Cyto_CGH+SNP_Microarray_4x180K_085591_D_BED_20200302.bed >hg38.GenetiSure_Cyto_CGH+SNP_Microarray_4x180K_085591_D_BED_20200302.uniq.bed +bedToBigBed hg38.GenetiSure_Cyto_CGH+SNP_Microarray_4x180K_085591_D_BED_20200302.uniq.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 +uniq hg38.GenetiSure_Cyto_CGH_Microarray_8x60K_085590_D_BED_20200302.bed > hg38.GenetiSure_Cyto_CGH_Microarray_8x60K_085590_D_BED_20200302.uniq.bed +bedToBigBed hg38.GenetiSure_Cyto_CGH_Microarray_8x60K_085590_D_BED_20200302.uniq.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 +uniq hg38.GenetiSure_Cyto_CGH_Microarray_4x180K_085589_D_BED_20200302.bed > hg38.GenetiSure_Cyto_CGH_Microarray_4x180K_085589_D_BED_20200302.uniq.bed +bedToBigBed hg38.GenetiSure_Cyto_CGH_Microarray_4x180K_085589_D_BED_20200302.uniq.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