Table 1.
Softwarea | Year | Main language | Assumption | Classifier | Training set | Result | URL |
---|---|---|---|---|---|---|---|
AnnotSV (Version: 3.3.6) | 2018 | Tcl, Shell, Python | ACMG | ACMG | Implementation of ACMG guideline. | Annotation, scores | https://lbgi.fr/AnnotSV/ |
CADD-SV (Version 1.1) | 2022 | Python, R | Evolutionary fitness | Random forest | Randomly distributed SVs over the human autosomes, evolutionarily fixed chimpanzee and human-derived SVs. | Scores | https://cadd-sv.bihealth.org/ |
ClassifyCNV (Version 1.1.1) | 2020 | Python, Shell | ACMG | ACMG | Implementation of ACMG guideline. | Scores | https://github.com/Genotek/ClassifyCNV |
dbCNV | 2023 | Perl, Shell | Molecular functions | Gradient boosted trees | The ClinVar, dbVar, ClinGen, DGV, DECIPHER and gnomAD (accessed before January 2023) | Classification | https://github.com/lllllv-1/dbCNV |
StrVCTVRE (Version 1.7) | 2022 | Python | Molecular functions on exons | Random forest | Rare SVs from ClinVar, gnomAD, and a recent great ape sequencing study. | Scores | https://strvctvre.berkeley.edu/ |
SVScore (Version 0.6) | 2017 | Perl, Shell | SNPs-based CADD scores | Derived from CADDb | The precomputed SNP scores generated by CADD v1.3 | Scores | https://github.com/lganel/SVScore |
TADA (Version 1.0.2) | 2022 | Python, Shell | Molecular functions related to long range interaction | Random forest | DECIPHER, Variants in the set published by Audano et al (2019), GnomAD, UK Biobank data set and DGV. | Scores | https://github.com/jakob-he/TADA/ |
XCNV | 2022 | R,Shell | Molecular functions | XGBoost | The dbVar, ClinGen, DECIPHER v10.1, and DGV (accessed before January 2021). | Scores | https://github.com/kbvstmd/XCNV |
Software version was given if available.
CADD was generated by the support vector machine.