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. 2024 Dec 10;8(3):e202402949. doi: 10.26508/lsa.202402949

Table 1.

Overview of the approaches evaluated in this work.

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
a

Software version was given if available.

b

CADD was generated by the support vector machine.