Note: Scoring of VCF files with CADD v1.7 is still rather slow if many new variants need to be calculated from scratch (e.g., if many insertion/deletion or multinucleotide subsitutions are included). If possible use the pre-scored whole genome and pre-calculated indel files directly where possible. We are very sorry for the inconvenience.

Retrieving SNV CADD scores via tabix

In theory, it is very simple to retrieve SNV CADD scores without downloading the whole genome data set via Tabix:

#Specify score file link
SCORE_FILE=https://krishna.gs.washington.edu/download/CADD/v1.4/GRCh37/whole_genome_SNVs_inclAnno.tsv.gz
#Download Tabix Index
INDEX=IndexFile
wget -c $SCORE_FILE.tbi -O $INDEX
#Retrieve variant scores
tabix $SCORE_FILE $INDEX 22:43451446-43451447

The CADD API for retrieving SNV scores

Please note that this API is still experimental and not thought to be used for retrieving thousands or millions 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 SNVs at a position with or without reference and alternate base and to retrieve all SNV in a genome range.

All API requests consist of a CADD version and the genome coordinate. The available CADD versions are v1.0 to v1.3, the two 1.4 releases GRCh37-v1.4 and GRCh38-v1.4, GRCh38-v1.5, GRCh37-v1.6 and GRCh38-v1.6, and latest releases GRCh37-v1.7 and GRCh38-v1.7. If you require annotations, you can add _inclAnno to the version string.

Single position access

The request path for SNV access is https://cadd.gs.washington.edu/api/v1.0/<CADD-version>/<chrom>:<pos> which returns a json list of the three SNV at that position:

curl -i https://cadd.gs.washington.edu/api/v1.0/v1.3/5:2003402

HTTP/1.0 200 OK
Content-Type: application/json
Content-Length: 410
Server: Werkzeug/0.11.15 Python/2.7.13
Date: Tue, 31 Jul 2018 19:04:18 GMT

[
  {
    "Alt": "A",
    "Chrom": "5",
    "PHRED": "0.850",
    "Pos": "2003402",
    "RawScore": "-0.251851",
    "Ref": "C"
  },
  ...
]

If you are requesting a single SNV with reference and alternate base given, you can do so via https://cadd.gs.washington.edu/api/v1.0/<CADD-version>/<chrom>:<pos>_<ref>_<alt> which returns just a single SNV object in a list. Note that this returns an empty list when ref or alt are not available.

Range access

Range access is similar to our web SNV-range access with the same limitation to 100 bases. It can be accessed via https://cadd.gs.washington.edu/api/v1.0/<chrom>:<start>-<end>. In contrast to the single position access, this returns a list of lists where the first item contains the field names.

curl -i https://cadd.gs.washington.edu/api/v1.0/GRCh38-v1.4/22:44044001-44044002

HTTP/1.0 200 OK
Content-Type: application/json
Content-Length: 615
Server: Werkzeug/0.11.15 Python/2.7.13
Date: Tue, 31 Jul 2018 19:17:44 GMT

[
  [
    "Chrom",
    "Pos",
    "Ref",
    "Alt",
    "RawScore",
    "PHRED"
  ],
  [
    "22",
    "44044001",
    "T",
    "A",
    "0.121712",
    "2.838"
  ],
  ...
]