Table 5.
Number of SNVs called by each of the four algorithms using raw and trimmed data
|
A. In raw data | |||
| |
≥ 3X* |
dbSNPs |
Non-dbSNPs |
|
SOAPsnp |
940 |
545 |
395 |
|
Atlas-SNP2 |
432 |
315 |
117 |
|
SAMtools |
532 |
376 |
156 |
|
GATK-UGT |
669 |
444 |
225 |
|
B. In trimmed data | |||
| |
≥ 3X* |
dbSNPs |
Non-dbSNPs |
|
SOAPsnp |
968 |
564 |
404 |
|
Atlas-SNP2 |
448 |
321 |
127 |
|
SAMtools |
570 |
398 |
172 |
| GATK-UGT | 729 | 478 | 251 |
* Atlas-SNP2 requires at least 3X to call a SNV. For the other three algorithms, we choose the called SNVs with ≥ 3X coverage.