9b06248769177714d1104ed0a8915e3641bd38cd
gperez2
  Wed Oct 9 15:00:21 2024 -0700
Adding and updating the CADD 1.7 track wrangled by Jeltje, refs #33940

diff --git src/hg/makeDb/doc/hg19.txt src/hg/makeDb/doc/hg19.txt
index 9e1b1aa..73a5eb3 100644
--- src/hg/makeDb/doc/hg19.txt
+++ src/hg/makeDb/doc/hg19.txt
@@ -35546,15 +35546,35 @@
 cd /hive/data/genomes/hg19/bed/ 
 mkdir abSplice; cd abSplice
 cp /cluster/home/jeltje/public_html/trackHubs/AbSplice_hub/hg19/AbSplice.bb .
 cp /cluster/home/jeltje/public_html/trackHubs/AbSplice_hub/hg19/description.html .
 cp /cluster/home/jeltje/public_html/trackHubs/AbSplice_hub/hg19/trackDb.txt .
 mv description.html abSplice.html
 mv trackDb.txt abSplice.ra
 cp abSplice.html ~/kent/src/hg/makeDb/trackDb/human/hg19
 cp abSplice.ra ~/kent/src/hg/makeDb/trackDb/human/hg19
 cd /gbdb/hg19/
 mkdir abSplice; cd abSplice
 ln -s /hive/data/genomes/hg19/bed/abSplice/AbSplice.bb
 cd ~/kent/src/hg/makeDb/trackDb/human/hg19
 vi abSplice.ra #Indented subtracks, changed bigDataUrl, adding group phenDis and html line
 ##############################################################################
+# CADD Jeltje Fri Sep 13 11:22:19 PDT 2024
+cd /hive/data/genomes/hg19/bed/cadd/v1.7
+aria2c -x4 -c https://kircherlab.bihealth.org/download/CADD/v1.7/GRCh37/whole_genome_SNVs.tsv.gz
+aria2c -x4 -c https://kircherlab.bihealth.org/download/CADD/v1.7/GRCh37/gnomad.genomes-exomes.r4.0.indel.tsv.gz
+python ~/kent/src/hg/makeDb/cadd/caddToBed.py gnomad.genomes-exomes.r4.0.indel.tsv.gz
+python ~/kent/src/hg/makeDb/cadd/caddToWig.py
+bedSort del.bed del.bed
+bedSort ins.bed ins.bed
+bedToBigBed del.bed ../../../chrom.sizes del.bb -type=bed9+ -tab -as=${HOME}/kent/src/hg/makeDb/cadd/cadd.as &
+bedToBigBed ins.bed ../../../chrom.sizes ins.bb -type=bed9+ -tab -as=${HOME}/kent/src/hg/makeDb/cadd/cadd.as &
+wigToBigWig a.wig ../../../chrom.sizes a.bw &
+wigToBigWig c.wig ../../../chrom.sizes c.bw &
+wigToBigWig g.wig ../../../chrom.sizes g.bw &
+wigToBigWig t.wig ../../../chrom.sizes t.bw &
+rm -f *.wig *.bed
+# as per note from v1.6
+mkdir /usr/local/apache/htdocs-hgdownload/goldenPath/archive/hg19/cadd/1.7
+cd /usr/local/apache/htdocs-hgdownload/goldenPath/archive/hg19/cadd/1.7
+cp /hive/data/genomes/hg19/bed/cadd/v1.7/*.b[bw] .
+##############################################################################