Retrieving SNV CADD scores via tabix

Pre-scored CADD-SV scores can be obtained without downloading the whole genome data set via Tabix:

#Specify score file link
SCORE_FILE=https://kircherlab.bihealth.org/download/CADD-SV/v1.1/prescored_variants.tsv.gz
#Download Tabix Index
INDEX=IndexFile
wget -c $SCORE_FILE.tbi -O $INDEX
#Retrieve variant scores
tabix $SCORE_FILE $INDEX chr22:43401446-43451447

The CADD API for retrieving SV scores

Please note that this API is still experimental and not thought to be used for retrieving thousands of variants. For extensive use, please use our online or offline scoring or contact us. Thank you!

In addition to retrieving CADD scores via tabix (see above), we also provide a webAPI. It is currently possible to retrieve SV genome ranges.

All API requests consist of a genome build, a CADD-SV version and the genome coordinates. The available genome builds are NCBI36, GRCh37 and GRCh38. Two CADD-SV versions are available (v1.0 and v1.1). If this information is omitted, version v1.0 is used. If you require annotations, you can add _inclAnno to the version string.

Range access

Range access is similar to our web SV-range. It can be accessed via https://cadd-sv.bihealth.org/api/v1.0/api/v1.0/<build>-<version>_<inclAnno>/<chrom>:<start>-<end>. This returns a list of lists where the first item contains the field/column names.

curl -i https://cadd-sv.bihealth.org/api/v1.0/GRCh38-v1.1/22:44034001-44044002
HTTP/2 200 
content-type: application/json
date: Fri, 24 Apr 2021 08:30:00 GMT
server: nginx/1.17.9
content-length: 250

[
  ["Chrom",
   "Start",
   "End",
   "Type",
   "Name",
   "CADD-SV-score",
   "Raw-Score_span",
   "Raw-Score_flank"],
  ["22",
   "43463338",
   "44099255",
   "DUP",
   "Abel_HJ_2020_DUP_chr22:43463338-44099255",
   "0.85825",
   "0.325710522039198",
   "0.0744504542742403"],
  ["22",
   "44031278",
   "44039850",
   "DEL",
   "1000G_DEL_chr22:44031278-44039850",
   "0.8724",
   "0.0960074624179696",
   "-0.0201758292924031"],
  ["22",
   "44031434",
   "44039865",
   "DEL",
   "gnomAD_DEL_chr22:44031434-44039865",
   "0.8837",
   "0.11550544812016",
   "-0.0140895534818769"],
  ["22",
   "44035794",
   "44041648",
   "DUP",
   "Abel_HJ_2020_DUP_chr22:44035794-44041648",
   "0.1785",
   "0.0197340170489945",
   "-0.191922206356091"]
]