1049c9c012c170c8ae3f2d7ebcbfa5019356b551 dschmelt Fri Mar 11 12:20:43 2022 -0800 Adding SNP/CNV array track refs #23591 diff --git src/hg/makeDb/doc/hg38/hg38.txt src/hg/makeDb/doc/hg38/hg38.txt index 1fe1747..5ad8e9b 100644 --- src/hg/makeDb/doc/hg38/hg38.txt +++ src/hg/makeDb/doc/hg38/hg38.txt @@ -6980,15 +6980,32 @@ mv region_hg38.bb CNVregions.bb cd /gbdb/hg38 mkdir panelApp cd panelApp ln -s /hive/data/genomes/hg38/bed/panelApp/genesPanel.bb ln -s /hive/data/genomes/hg38/bed/panelApp/STRsPanel.bb 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 +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