<commit_before>#~~~Template configuration file to run iCallSV~~~#
#### Path to python executable ###
[Python]
PYTHON:
#### Path to R executable and R Lib ###
[R]
RHOME:
RLIB:
#### Path to delly, bcftools executables and Version of delly (supports only 0.7.3)###
[SVcaller]
DELLY:
DellyVersion:
BCFTOOLS:
#### Path to hg19 Referece Fasta file ###
[ReferenceFasta]
REFFASTA:
#### Path to file containing regions to exclude please follow Delly documentation for this ###
[ExcludeRegion]
EXREGIONS:
#### Path to file containing regions to where lenient threshold will be used; and file containing genes to keep ###
[HotSpotRegions]
HotspotFile:
GenesToKeep:
#### Path to file containing regions/genes to filter ###
[BlackListRegions]
BlackListFile:
BlackListGenes:
#### Path to samtools executable ###
[SAMTOOLS]
SAMTOOLS:
#### Path to iAnnotateSV.py and all its required files, please follow iAnnotateSV documentation ###
[iAnnotateSV]
ANNOSV:
GENOMEBUILD:
DISTANCE:
CANONICALTRANSCRIPTFILE:
UNIPROTFILE:
CosmicCensus:
CosmicFusionCounts:
RepeatRegionAnnotation:
DGvAnnotations:
#### TargetSeqView Parameters ###
[TargetSeqView]
CalculateConfidenceScore:
GENOMEBUILD:
ReadLength:
#### Parameters to run Delly ###
[ParametersToRunDelly]
MAPQ: 20
NumberOfProcessors: 4
[ParametersToFilterDellyResults]
####Case Allele Fraction Hotspot####
CaseAltFreqHotspot: 0.05
####Total Case Coverage Hotspot#####
CaseCoverageHotspot = 5
####Control Allele Fraction Hotspot####
ControlAltFreqHotspot = 0
####Case Allele Fraction####
CaseAltFreq: 0.10
####Total Case Coverage#####
CaseCoverage = 10
####Control Allele Fraction####
ControlAltFreq = 0
###Overall Supporting Read-pairs ###
OverallSupportingReads: 5
###Overall Supporting Read-pairs Hotspot ###
OverallSupportingReadsHotspot: 3
###Overall Supporting splitreads ###
OverallSupportingSplitReads: 0
###Overall Supporting splitreads Hotspot ###
OverallSupportingSplitReadsHotspot: 0
###Case Supporting Read-pairs ###
CaseSupportingReads: 2
###Case Supporting splitreads ###
CaseSupportingSplitReads: 0
###Case Supporting Read-pairs Hotspot ###
CaseSupportingReadsHotspot: 1
###Case Supporting splitreads Hotspot ###
CaseSupportingSplitReadsHotspot: 0
###Control Supporting Read-pairs ###
ControlSupportingReads: 3
###Control Supporting Read-pairs Hotspot ###
ControlSupportingReadsHotspot: 3
###Control Supporting splitreads ###
ControlSupportingSplitReads: 3
###Control Supporting splitreads Hotspot ###
ControlSupportingSplitReadsHotspot: 3
###Length of Structural Variant###
LengthOfSV: 500
###Overall Mapping Quality Threshold###
OverallMapq: 20
###Overall Mapping Quality Threshold Hotspot###
OverallMapqHotspot: 5<commit_msg>Updated config file to be consistent.<commit_after>#~~~Template configuration file to run iCallSV~~~#
#### Path to python executable ###
[Python]
PYTHON:
#### Path to R executable and R Lib ###
[R]
RHOME:
RLIB:
#### Path to delly, bcftools executables and Version of delly (supports only 0.7.3)###
[SVcaller]
DELLY:
DellyVersion:
BCFTOOLS:
#### Path to hg19 Referece Fasta file ###
[ReferenceFasta]
REFFASTA:
#### Path to file containing regions to exclude please follow Delly documentation for this ###
[ExcludeRegion]
EXREGIONS:
#### Path to file containing regions to where lenient threshold will be used; and file containing genes to keep ###
[HotSpotRegions]
HotspotFile:
GenesToKeep:
#### Path to file containing regions/genes to filter ###
[BlackListRegions]
BlackListFile:
BlackListGenes:
#### Path to samtools executable ###
[SAMTOOLS]
SAMTOOLS:
#### Path to iAnnotateSV.py and all its required files, please follow iAnnotateSV documentation ###
[iAnnotateSV]
ANNOSV:
GENOMEBUILD:
DISTANCE:
CANONICALTRANSCRIPTFILE:
UNIPROTFILE:
CosmicCensus:
CosmicFusionCounts:
RepeatRegionAnnotation:
DGvAnnotations:
#### TargetSeqView Parameters ###
[TargetSeqView]
CalculateConfidenceScore:
GENOMEBUILD:
ReadLength:
#### Parameters to run Delly ###
[ParametersToRunDelly]
MAPQ: 20
NumberOfProcessors: 4
[ParametersToFilterDellyResults]
####Case Allele Fraction Hotspot####
CaseAltFreqHotspot: 0.05
####Total Case Coverage Hotspot#####
CaseCoverageHotspot: 5
####Control Allele Fraction Hotspot####
ControlAltFreqHotspot: 0
####Case Allele Fraction####
CaseAltFreq: 0.10
####Total Case Coverage#####
CaseCoverage: 10
####Control Allele Fraction####
ControlAltFreq: 0
###Overall Supporting Read-pairs ###
OverallSupportingReads: 5
###Overall Supporting Read-pairs Hotspot ###
OverallSupportingReadsHotspot: 3
###Overall Supporting splitreads ###
OverallSupportingSplitReads: 0
###Overall Supporting splitreads Hotspot ###
OverallSupportingSplitReadsHotspot: 0
###Case Supporting Read-pairs ###
CaseSupportingReads: 2
###Case Supporting splitreads ###
CaseSupportingSplitReads: 0
###Case Supporting Read-pairs Hotspot ###
CaseSupportingReadsHotspot: 1
###Case Supporting splitreads Hotspot ###
CaseSupportingSplitReadsHotspot: 0
###Control Supporting Read-pairs ###
ControlSupportingReads: 3
###Control Supporting Read-pairs Hotspot ###
ControlSupportingReadsHotspot: 3
###Control Supporting splitreads ###
ControlSupportingSplitReads: 3
###Control Supporting splitreads Hotspot ###
ControlSupportingSplitReadsHotspot: 3
###Length of Structural Variant###
LengthOfSV: 500
###Overall Mapping Quality Threshold###
OverallMapq: 20
###Overall Mapping Quality Threshold Hotspot###
OverallMapqHotspot: 5
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