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/hg38/cadd.txt src/hg/makeDb/doc/hg38/cadd.txt
index 778a032..c5c4765 100644
--- src/hg/makeDb/doc/hg38/cadd.txt
+++ src/hg/makeDb/doc/hg38/cadd.txt
@@ -1,17 +1,35 @@
 # CADD track, #18492, from CADD track hub
 Thu Dec  5 06:15:48 PST 2019 (max)
 mkdir -p /hive/data/genomes/{hg19,hg38}/bed/cadd/
 cd /hive/data/genomes/hg38/bed/cadd
 wget https://krishna.gs.washington.edu/download/CADD/v1.6/GRCh38/whole_genome_SNVs.tsv.gz
 wget https://krishna.gs.washington.edu/download/CADD/v1.6/GRCh38/gnomad.genomes.r3.0.indel.tsv.gz
 time python ~/kent/src/hg/makeDb/cadd/caddToWig.py
 time python ~/kent/src/hg/makeDb/cadd/caddToBed.py gnomad.genomes.r3.0.indel.tsv.gz
 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 &
 # make sure that no error occured by checking the bw/bb files
+
+# CADD1_7 track, #33940
+Fri Sep 13 11:09:57 PDT 2024 (jeltje)
+mkdir -p /hive/data/genomes/{hg19,hg38}/bed/cadd/v1.7
+cd /hive/data/genomes/hg38/bed/cadd/v1.7
+aria2c -x4 -c https://kircherlab.bihealth.org/download/CADD/v1.7/GRCh38/whole_genome_SNVs.tsv.gz
+aria2c -x4 -c https://kircherlab.bihealth.org/download/CADD/v1.7/GRCh38/gnomad.genomes.r4.0.indel.tsv.gz
+python ~/kent/src/hg/makeDb/cadd/caddToWig.py whole_genome_SNVs.tsv.gz
+python ~/kent/src/hg/makeDb/cadd/caddToWig.py
+python ~/kent/src/hg/makeDb/cadd/caddToBed.py gnomad.genomes.r4.0.indel.tsv.gz
+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 &