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.
Tools and applications using/annotating CADD
- gnomAD and ExAC: variants aggregated from disease controls, late onset disease studies and population studies
- Bravo/TOPMed: variants from WGS variant calls aggregated across various cohort studies
- Ensembl VEP: genome variant annotation tool and platform
- dbNSFP: database for many different annotations and scores for non-synonymous sequence alterations
- PopViz: webserver for visualizing minor allele frequencies and damage prediction scores of human genetic variations
Annotations
Selection of links to (some) annotations that have been added since CADD v1.4. For more information about annotations included in CADD please also see our manuscripts and release notes.
- TargetScan
- dbscSNV
- SpliceAI
- MMSplice
- Meta Evolutionary Scale Modeling (ESM) language models for proteins
- GRCh38/hg38 GERP, PhastCons and PhyloP: using muliz*way alignment from UCSC, processing according to UCSC/Kentlab without human
- GRCh37/hg19 GERP
- Encode Annotations, using data from reference epigenomes like this
- ChromHMM: in GRCh38 using 25 state Roadmap/Encode model
- Ensembl Regulatroy Build v90 from Ensembl server
- ReMap2 (ReMap2018)