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: rmdup; version: 0.1.19-44428cd)
SAMtools(subprogram: filter; version: 0.1.19-44428cd)
SAMtools(subprogram: index; version: 0.1.19-44428cd)
SAMtools(subprogram: mpileup; version: 0.1.19-44428cd)
| Options | Values |
|---|
| minDepth |
10 |
| minMapQBias |
0 |
| FILTERadditional |
|
| BCFadditional |
|
| minStrandBias |
0.0001 |
| bwaDownGrade |
50 |
| minEndDistBias |
0.0001 |
| minBaseQBias |
1e-100 |
| SAMadditional |
|
| originalBAM |
1 |