Analysis Steps and Parameters
DISABLED steps are NOT shown here.
FastQC(version: 0.10.1)
BWA-MEM(version: 0.7.8-r455)
| Options | Values |
|---|
| gapOpenPenalty |
6 |
| clipPenalty |
5 |
| additional |
|
| gapExtensionPenalty |
1 |
| matchScore |
1 |
| readSingletonPenalty |
17 |
| mismatchPenalty |
4 |
Picard(subprogram: markduplicates; version: 1.112)
SAMtools(subprogram: filter; version: 0.1.19-44428cd)
SAMtools(subprogram: index; version: 0.1.19-44428cd)
GATK-Full(subprogram: realign; version: 3.1-1-g07a4bf8)
| Options | Values |
|---|
| maxInMemory |
200000 |
| additional |
-rf NotPrimaryAlignment --consensusDeterminationModel USE_READS -l ERROR |
| LOD |
0.4 |
GATK-Full(subprogram: recal; version: 3.1-1-g07a4bf8)
| Options | Values |
|---|
| additional |
--disable_indel_quals -rf BadCigar -l ERROR |
| covariates |
ReadGroupCovariate,QualityScoreCovariate,ContextCovariate,CycleCovariate |
GATK-Full(subprogram: HaplotypeCaller; version: 3.1-1-g07a4bf8)
| Options | Values |
|---|
| numBadVariants |
5000 |
| forceINDELVQSR |
0 |
| indelMaxGaussians |
4 |
| snpfilters |
QDFilter,QD<2.0 FSFilter,FS>60.0;MQFilter,MQ<40.0;MaqQualRankSumFilter,MappingQualityRankSum<-12.5;ReadPosFilter,ReadPosRankSum<-8.0 |
| originalBAM |
0 |
| HCadditional |
-rf BadCigar -l ERROR |
| maxGaussians |
4 |
| filter |
1 |
| indeltsfilter |
99.0 |
| forceSNPVQSR |
0 |
| indelfilters |
QDFilter,QD<2.0 ReadPosFilter,ReadPosRankSum<-20.0;FSFilter,FS>200.0 |
| annotations |
QD,MQRankSum,ReadPosRankSum,FS,MQ |
| indelNumBadVariants |
1000 |
| indelAnnotations |
DP,FS,MQRankSum,ReadPosRankSum |
| snptsfilter |
99.0 |
| clusterWindowSize |
10 |
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 |
VarScan(version: 2.3)
| Options | Values |
|---|
| minDepth |
10 |
| VARadditional |
|
| minBaseQ |
20 |
| P |
0.1 |
| minSupport |
2 |
| SAMadditional |
|
| originalBAM |
1 |