Analysis Steps and Parameters
DISABLED steps are NOT shown here.
FastQC(version: 0.11.2)
BWA-MEM(version: 0.7.8-r455)
| Options | Values |
|---|
| gapOpenPenalty |
6 |
| clipPenalty |
5 |
| additional |
|
| gapExtensionPenalty |
1 |
| matchScore |
1 |
| readSingletonPenalty |
17 |
| mismatchPenalty |
4 |
SAMtools(subprogram: filter; version: 0.1.19-44428cd)
SAMtools(subprogram: index; version: 0.1.19-44428cd)
VarScan(version: 2.3)
| Options | Values |
|---|
| VARSOMATICadditional |
--min-coverage-normal 8 --min-coverage-tumor 6 --normal-purity 1.00 --tumor-purity 1.00 --somatic-p-value 0.05 |
| minDepth |
10 |
| VARadditional |
|
| minBaseQ |
20 |
| P |
0.1 |
| minSupport |
2 |
| SAMadditional |
|
| originalBAM |
1 |