update to cadd v1.4
MODIFY
gemini/annotation_provenance/make-cadd.sh
gemini/annotation_provenance/make-cadd.sh
# Download the raw CADD TSV and Tabix index (no annotations, just scores)
+<<DOCS
wget http://krishna.gs.washington.edu/download/CADD/v1.0/whole_genome_SNVs.tsv.gz
wget http://krishna.gs.washington.edu/download/CADD/v1.0/whole_genome_SNVs.tsv.gz.tbi
# E.g snippet of contents in the above file
ChromPosRefAltRawScorePHRED
110002AC-0.6412591.170
-1 10002 A G -0.647307 1.149
-1 10002 A T -0.533326 1.574
+17010002AG-0.6473071.149
+14910002AT-0.5333261.574
#compress columns 5 & 6 to collapse values for all possible 'Alt' for a given position
# as (lexically ordered) comma separated values, using Bedtools
# compress float values to 2 decimal precision
#resultant compression would look like this
-Chrom Pos Ref RawScore PHRED
-1 10002 A -0.64,-0.65,-0.53 1.17,1.15,1.57
+ChromPosRefAltRawScorePHREDPosRefRawScorePHRED
+14910002AT10002A-0.64,-0.65,-0.53332611.17,1.15,1.57
+DOCS
+set -euo pipefail
-wget -O - http://krishna.gs.washington.edu/download/CADD/v1.3/whole_genome_SNVs.tsv.gz \
- | zgrep -v ^# \
+#wget -c https://krishna.gs.washington.edu/download/CADD/v1.4/GRCh37/whole_genome_SNVs.tsv.gz
+wget -c http://krishna.gs.washington.edu/download/CADD/v1.4/GRCh37/InDels.tsv.gz
+
+zgrep -v ^# whole_genome_SNVs.tsv.gz \
| awk '{printf("%s\t%d\t%s\t%s\t%0.2f\t%0.2f\n",$1,$2,$3,$4,$5,$6)}' \
- | bedtools groupby -g 1,2,3 -c 5,6 -o collapse,collapse | bgzip -c > whole_genome_SNVs.tsv.compressed.gz
-tabix -b 2 -e 2 whole_genome_SNVs.tsv.compressed.gz
+ | bedtools groupby -g 1,2,3 -c 5,6 -o collapse,collapse \
+ | sort -k1,1 -k2,2n \
+ | bgzip -l 7 -c > caddv1.4.compressed.gz
+tabix -b 2 -e 2 caddv1.4.compressed.gz

MODIFY
gemini/annotations.py
gemini/annotations.py
@@ -60,8 +60,8 @@ def get_anno_files(args):
# optional annotations
if os.path.exists(os.path.join(anno_dirname, 'hg19.gerp.bw')):
annos['gerp_bp'] = os.path.join(anno_dirname, 'hg19.gerp.bw')
- if os.path.exists(os.path.join(anno_dirname, 'whole_genome_SNVs.tsv.compressed.gz')):
- annos['cadd_score'] = os.path.join(anno_dirname, 'whole_genome_SNVs.tsv.compressed.gz')
+ if os.path.exists(os.path.join(anno_dirname, 'caddv1.4.compressed.gz')):
+ annos['cadd_score'] = os.path.join(anno_dirname, 'caddv1.4.compressed.gz')
return annos
class ClinVarInfo(object):

MODIFY
gemini/install-data.py
gemini/install-data.py
@@ -55,7 +55,7 @@ anno_files = \
'gnomad.exomes.r2.1.tidy.bcf',
'geno2mp.variants.tidy.vcf.gz',
]
-extra_anno_files = {"gerp_bp": "hg19.gerp.bw", "cadd_score": "whole_genome_SNVs.tsv.compressed.gz"}
+extra_anno_files = {"gerp_bp": "hg19.gerp.bw", "cadd_score": "caddv1.4.compressed.gz"}
custom_downloads = {}
@@ -71,7 +71,6 @@ anno_versions = {
"ESP6500SI.all.snps_indels.tidy.v2.vcf.gz": 2,
'ExAC.r0.3.sites.vep.tidy.vcf.gz': 4,
'geno2mp.variants.tidy.vcf.gz': 1,
- "whole_genome_SNVs.tsv.compressed.gz": 2,
}
def install_annotation_files(anno_root_dir, dl_files=False, extra=None):

MODIFY
test/test-cadd.sh
test/test-cadd.sh
gemini load -v test.cadd.vcf --skip-gerp-bp test.cadd.db > /dev/null 2>&1
path=`gemini_python ../gemini/anno_info.py`
-file="whole_genome_SNVs.tsv.compressed.gz"
+file="caddv1.4.compressed.gz"
if [ -f $path/$file ]; then

update to cadd v1.4