| Exonic SNVs | Exonic indels | Intronic SNVs | |||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
MCC | d | TPR | FPR | MCC | d | TPR | FPR | MCC | d | TPR | FPR | |
Null interval padding | ||||||||||||
BWA-MEM/GATK-HC | 0.832 | 0.563 | 0.985 | 0.189 | 1.000 | 0.707 | 1.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
BWA-MEM/GATK-UG | 0.956 | 0.665 | 0.997 | 0.057 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
BWA-MEM/SAMtools | 0.945 | 0.663 | 0.994 | 0.057 | 1.000 | 0.707 | 1.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
Bowtie2/GATK-HC | 0.672 | 0.608 | 0.860 | 0.000 | 1.000 | 0.707 | 1.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
Bowtie2/GATK-UG | 0.300 | 0.167 | 0.953 | 0.717 | 0.000 | 0.000 | 0.000 | 0.000 | − 0.332 | − 0.088 | 0.000 | 0.125 |
Bowtie2/SAMtools | 0.748 | 0.524 | 0.968 | 0.226 | 1.000 | 0.707 | 1.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
Stampy/GATK-HC | 0.819 | 0.550 | 0.985 | 0.208 | 1.000 | 0.707 | 1.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
Stampy/GATK-UG | 0.852 | 0.556 | 0.994 | 0.208 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
Stampy/SAMtools | 0.946 | 0.674 | 0.991 | 0.038 | 1.000 | 0.707 | 1.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
50Â bp interval padding | ||||||||||||
BWA-MEM/GATK-HC | 0.819 | 0.550 | 0.985 | 0.208 | 1.000 | 0.707 | 1.000 | 0.000 | 0.828 | 0.666 | 0.942 | 0.000 |
BWA-MEM/GATK-UG | 0.956 | 0.665 | 0.997 | 0.057 | 0.00 | 0.000 | 0.000 | 0.000 | 0.701 | 0.564 | 0.923 | 0.125 |
BWA-MEM/SAMtools | 0.946 | 0.674 | 0.991 | 0.038 | 1.000 | 0.707 | 1.000 | 0.000 | 0.711 | 0.626 | 0.885 | 0.000 |
Bowtie2/GATK-HC | 0.647 | 0.582 | 0.860 | 0.038 | 1.000 | 0.707 | 1.000 | 0.000 | 0.576 | 0.558 | 0.789 | 0.000 |
Bowtie2/GATK-UG | 0.311 | 0.178 | 0.950 | 0.698 | 0.000 | 0.000 | 0.000 | 0.000 | − 0.074 | − 0.061 | 0.789 | 0.875 |
Bowtie2/SAMtools | 0.767 | 0.529 | 0.974 | 0.226 | 1.000 | 0.707 | 1.000 | 0.000 | 0.515 | 0.483 | 0.808 | 0.125 |
Stampy/GATK-HC | 0.819 | 0.550 | 0.985 | 0.208 | 1.000 | 0.707 | 1.000 | 0.000 | 0.828 | 0.666 | 0.942 | 0.000 |
Stampy/GATK-UG | 0.852 | 0.545 | 0.997 | 0.226 | 0.000 | 0.000 | 0.000 | 0.000 | 0.574 | 0.462 | 0.904 | 0.250 |
Stampy/SAMtools | 0.968 | 0.690 | 0.994 | 0.019 | 1.000 | 0.707 | 1.000 | 0.000 | 0.595 | 0.524 | 0.865 | 0.125 |
100Â bp interval padding | ||||||||||||
BWA-MEM/GATK-HC | 0.831 | 0.563 | 0.985 | 0.189 | 1.000 | 0.707 | 1.000 | 0.000 | 0.828 | 0.666 | 0.942 | 0.000 |
BWA-MEM/GATK-UG | 0.934 | 0.650 | 0.994 | 0.075 | 0.000 | 0.000 | 0.000 | 0.000 | 0.746 | 0.578 | 0.942 | 0.125 |
BWA-MEM/SAMtools | 0.956 | 0.676 | 0.994 | 0.038 | 1.000 | 0.707 | 1.000 | 0.000 | 0.711 | 0.626 | 0.885 | 0.000 |
Bowtie2/GATK-HC | 0.647 | 0.582 | 0.860 | 0.038 | 1.000 | 0.707 | 1.000 | 0.000 | 0.576 | 0.558 | 0.789 | 0.000 |
Bowtie2/GATK-UG | 0.338 | 0.194 | 0.953 | 0.679 | 0.000 | 0.000 | 0.000 | 0.000 | − 0.059 | − 0.048 | 0.808 | 0.875 |
Bowtie2/SAMtools | 0.753 | 0.515 | 0.974 | 0.245 | 1.000 | 0.707 | 1.000 | 0.000 | 0.540 | 0.496 | 0.827 | 0.125 |
Stampy/GATK-HC | 0.831 | 0.563 | 0.985 | 0.189 | 1.000 | 0.707 | 1.000 | 0.000 | 0.828 | 0.666 | 0.942 | 0.000 |
Stampy/GATK-UG | 0.852 | 0.556 | 0.994 | 0.208 | 0.000 | 0.000 | 0.000 | 0.000 | 0.574 | 0.462 | 0.904 | 0.250 |
Stampy/SAMtools | 0.945 | 0.663 | 0.994 | 0.057 | 1.000 | 0.707 | 1.000 | 0.000 | 0.679 | 0.612 | 0.865 | 0.000 |
BWA Enrichment | 0.956 | 0.676 | 0.994 | 0.038 | 1.000 | 0.707 | 1.000 | 0.000 | − 0.331 | − 0.088 | 0.000 | 0.1250 |
 | Intronic indels | All types of variants | ||||||
---|---|---|---|---|---|---|---|---|
 | MCC | d | TPR | FPR | MCC | d | TPR | FPR |
Null interval padding | ||||||||
BWA-MEM/GATK-HC | 0.000 | 0.000 | 0.000 | 0.000 | 0.581 | 0.502 | 0.848 | 0.139 |
BWA-MEM/GATK-UG | 0.000 | 0.000 | 0.000 | 0.000 | 0.653 | 0.572 | 0.851 | 0.042 |
BWA-MEM/SAMtools | 0.000 | 0.000 | 0.000 | 0.000 | 0.660 | 0.576 | 0.856 | 0.042 |
Bowtie2/GATK-HC | 0.000 | 0.000 | 0.000 | 0.000 | 0.551 | 0.524 | 0.741 | 0.000 |
Bowtie2/GATK-UG | 0.000 | 0.000 | 0.000 | 0.000 | 0.233 | 0.192 | 0.813 | 0.542 |
Bowtie2/SAMtools | 0.000 | 0.000 | 0.000 | 0.000 | 0.540 | 0.471 | 0.833 | 0.167 |
Stampy/GATK-HC | 0.000 | 0.000 | 0.000 | 0.000 | 0.571 | 0.492 | 0.848 | 0.153 |
Stampy/GATK-UG | 0.000 | 0.000 | 0.000 | 0.000 | 0.571 | 0.492 | 0.848 | 0.153 |
Stampy/SAMtools | 0.000 | 0.000 | 0.000 | 0.000 | 0.666 | 0.584 | 0.853 | 0.028 |
50Â bp interval padding | ||||||||
BWA-MEM/GATK-HC | 0.000 | 0.000 | 1.000 | 1.000 | 0.749 | 0.487 | 0.980 | 0.292 |
BWA-MEM/GATK-UG | 0.000 | 0.000 | 0.000 | 0.000 | 0.898 | 0.652 | 0.978 | 0.056 |
BWA-MEM/SAMtools | 0.674 | 0.354 | 0.500 | 0.000 | 0.908 | 0.670 | 0.975 | 0.028 |
Bowtie2/GATK-HC | 0.200 | 0.414 | 1.000 | 0.800 | 0.588 | 0.505 | 0.853 | 0.139 |
Bowtie2/GATK-UG | 0.000 | 0.000 | 0.000 | 0.000 | 0.321 | 0.209 | 0.920 | 0.625 |
Bowtie2/SAMtools | 0.674 | 0.354 | 0.500 | 0.000 | 0.741 | 0.544 | 0.950 | 0.181 |
Stampy/GATK-HC | 0.135 | 0.071 | 1.000 | 0.900 | 0.758 | 0.497 | 0.980 | 0.278 |
Stampy/GATK-UG | 0.000 | 0.000 | 0.000 | 0.000 | 0.790 | 0.542 | 0.975 | 0.208 |
Stampy/SAMtools | 0.674 | 0.354 | 0.500 | 0.000 | 0.908 | 0.670 | 0.975 | 0.028 |
100Â bp interval padding | ||||||||
BWA-MEM/GATK-HC | 0.200 | 0.414 | 1.000 | 0.800 | 0.777 | 0.516 | 0.980 | 0.250 |
BWA-MEM/GATK-UG | 0.00 | 0.000 | 0.000 | 0.000 | 0.888 | 0.642 | 0.978 | 0.069 |
BWA-MEM/SAMtools | 0.674 | 0.354 | 0.500 | 0.000 | 0.922 | 0.673 | 0.980 | 0.028 |
Bowtie2/GATK-HC | 0.200 | 0.414 | 1.000 | 0.800 | 0.588 | 0.505 | 0.853 | 0.139 |
Bowtie2/GATK-UG | 0.000 | 0.000 | 0.000 | 0.000 | 0.344 | 0.222 | 0.925 | 0.611 |
Bowtie2/SAMtools | 0.674 | 0.354 | 0.500 | 0.000 | 0.744 | 0.538 | 0.955 | 0.194 |
Stampy/GATK-HC | 0.000 | 0.000 | 1.000 | 1.000 | 0.758 | 0.497 | 0.980 | 0.278 |
Stampy/GATK-UG | 0.000 | 0.000 | 0.000 | 0.000 | 0.792 | 0.550 | 0.973 | 0.194 |
Stampy/SAMtools | 0.674 | 0.354 | 0.500 | 0.000 | 0.906 | 0.662 | 0.978 | 0.042 |
BWA Enrichment | 0.000 | 0.000 | 0.000 | 0.000 | 0.663 | 0.577 | 0.858 | 0.042 |