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)
GATKLite(subprogram: realign; version: 2.3-9-gdcdccbb)
| Options | Values |
|---|
| maxInMemory |
200000 |
| additional |
-rf NotPrimaryAlignment -l ERROR |
GATKLite(subprogram: variant; version: 2.3-9-gdcdccbb)
| Options | Values |
|---|
| indelPercentBadVariants |
0.05 |
| numBadVariants |
5000 |
| UGadditional |
-rf BadCigar --genotype_likelihoods_model BOTH -l ERROR |
| forceINDELVQSR |
0 |
| indelMaxGaussians |
4 |
| snpfilters |
QDFilter,QD<2.0 FSFilter,FS>60.0;MQFilter,MQ<40.0;HaploFilter,HaplotypeScore>13.0;MaqQualRankSumFilter,MappingQualityRankSum<-12.5;ReadPosFilter,ReadPosRankSum<-8.0 |
| originalBAM |
0 |
| filter |
1 |
| maxGaussians |
4 |
| indeltsfilter |
99.0 |
| annotations |
QD,HaplotypeScore,MQRankSum,ReadPosRankSum,FS,MQ |
| indelfilters |
QDFilter,QD<2.0 ReadPosFilter,ReadPosRankSum<-20.0;FSFilter,FS>200.0 |
| forceSNPVQSR |
0 |
| indelNumBadVariants |
1000 |
| indelAnnotations |
DP,FS,MQRankSum,ReadPosRankSum |
| snptsfilter |
99.0 |
| clusterWindowSize |
10 |
| percentBadVariants |
0.05 |
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 |
FreeBayes(version: 0.9.14-14-gb00b735-dirty)
| Options | Values |
|---|
| minBaseQual |
10 |
| maxSNP |
5 |
| minMapQual |
30 |
| minDepth |
10 |
| maxINDEL |
5 |
| additional |
|
| originalBAM |
1 |
| maxMismatchFraction |
0.5 |