| Code |
C |
Perl |
C++ |
Java |
Java |
| Model |
HMM & MAQ |
16-genotype probabilistic |
Bayesian |
heuristic algorithm |
Bayesian |
| Sampling |
Single & multiple |
Single |
Single |
Single & multiple |
Single & multiple |
| Variants |
SNPs & indels |
SNPs & indels |
SNPs & indels&MNPs |
SNPs & indels |
SNPs & indels |
| Features |
Sorting, indexing, etc. |
easy to use, timesaving |
straightforward |
meet desired thresholds for read depth, base quality, variant allele frequency, and statistical significance |
Realignment, per base recalibration, VQSR |
| Reference |
Danecek et al., 2017 [15] |
Luo et al., 2017 [19] |
Garrison and Marth, 2012 [18] |
Koboldt et al., 2012 [16] |
Mckenna et al., 2010 [14] |
