Table 2 Pathogenicity predictors and default or recommended classification thresholds used in this study
Software | Input data format | Command line interface | Genome Build (GRCh) | Benign threshold | Pathogenic threshold |
|---|---|---|---|---|---|
CADD | VCF | + | 37/38 | < 20 | > = 20 |
CAPICE | VEP annotated TSV | + | 37/38 | < 0.02 | > = 0.02 |
FATHMM-indel | VCF | − | 37 | > = 0.5 | < 0.5 |
MutPred-Indel | Peptide (FASTA) | + | 37/38 | < 0.672 | > = 0.672 |
MutationTaster 2021 | VCF/genomic position/transcript specific | − | 37 | Benign | Deleterious |
PROVEAN | VCF subset (CSV) | + | 37 | > 2.5 | < = 2.5 |
SIFT-indel | VCF subset (CSV) | − | 37/38 | Neutral | Damaging |
VEST-indel | VCF | + | 37/38 | < 0.5 | > = 0.5 |
VVP | VCF | + | 37/38 | < 57 | > = 57 |