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Inputs for SVcalling
The following is an overview of all available inputs in SVcalling.
Required inputs
- SVcalling.bamFile
-
File
sorted BAM file - SVcalling.bamIndex
-
File
BAM index(.bai) file - SVcalling.bwaIndex
-
struct(fastaFile : File, indexFiles : Array[File])
Struct containing the BWA reference files - SVcalling.manta.cores
-
Int — Default:
1
The the number of cores required to run a program - SVcalling.manta.memoryGb
-
Int — Default:
4
The memory required to run the manta - SVcalling.referenceFasta
-
File
The reference fasta file - SVcalling.referenceFastaDict
-
File
Sequence dictionary (.dict) file of the reference - SVcalling.referenceFastaFai
-
File
Fasta index (.fai) file of the reference - SVcalling.sample
-
String
The name of the sample
Other common inputs
- SVcalling.manta.callRegions
-
File?
The bed file which indicates the regions to operate on. - SVcalling.manta.callRegionsIndex
-
File?
The index of the bed file which indicates the regions to operate on. - SVcalling.manta.exome
-
Boolean — Default:
false
Whether or not the data is from exome sequencing. - SVcalling.outputDir
-
String — Default:
"."
The directory the output should be written to.
Advanced inputs
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- SVcalling.clever.memory
-
String — Default:
"55G"
The memory required to run the programs - SVcalling.clever.threads
-
Int — Default:
10
The the number of threads required to run a program - SVcalling.clever.timeMinutes
-
Int — Default:
480
The maximum amount of time the job will run in minutes. - SVcalling.delly.memory
-
String — Default:
"15G"
The memory required to run the programs - SVcalling.delly.timeMinutes
-
Int — Default:
300
The maximum amount of time the job will run in minutes. - SVcalling.delly2vcf.compressionLevel
-
Int — Default:
1
Compression level from 0 (uncompressed) to 9 (best). - SVcalling.delly2vcf.memory
-
String — Default:
"256M"
The amount of memory this job will use. - SVcalling.delly2vcf.timeMinutes
-
Int — Default:
1 + ceil(size(inputFile,"G"))
The maximum amount of time the job will run in minutes. - SVcalling.dockerImages
-
Map[String,String] — Default:
{"bcftools": "quay.io/biocontainers/bcftools:1.10.2--h4f4756c_2", "clever": "quay.io/biocontainers/clever-toolkit:2.4--py36hcfe0e84_6", "delly": "quay.io/biocontainers/delly:0.8.1--h4037b6b_1", "manta": "quay.io/biocontainers/manta:1.4.0--py27_1", "picard": "quay.io/biocontainers/picard:2.23.2--0", "samtools": "quay.io/biocontainers/samtools:1.10--h9402c20_2", "survivor": "quay.io/biocontainers/survivor:1.0.6--h6bb024c_0", "smoove": "quay.io/biocontainers/smoove:0.2.5--0"}
A map describing the docker image used for the tasks. - SVcalling.FilterShortReadsBam.memory
-
String — Default:
"1G"
The amount of memory this job will use. - SVcalling.FilterShortReadsBam.timeMinutes
-
Int — Default:
1 + ceil((size(bamFile,"G") * 8))
The maximum amount of time the job will run in minutes. - SVcalling.manta.timeMinutes
-
Int — Default:
60
The maximum amount of time the job will run in minutes. - SVcalling.mateclever.cleverMaxDelLength
-
Int — Default:
100000
The maximum deletion length to look for in Clever predictions. - SVcalling.mateclever.maxLengthDiff
-
Int — Default:
30
The maximum length difference between split-read and read-pair deletion to be considered identical. - SVcalling.mateclever.maxOffset
-
Int — Default:
150
The maximum center distance between split-read and read-pair deletion to be considered identical. - SVcalling.mateclever.memory
-
String — Default:
"15G"
The memory required to run the programs - SVcalling.mateclever.threads
-
Int — Default:
10
The the number of threads required to run a program - SVcalling.mateclever.timeMinutes
-
Int — Default:
600
The maximum amount of time the job will run in minutes. - SVcalling.renameSample.javaXmx
-
String — Default:
"8G"
The max. memory allocated for JAVA - SVcalling.renameSample.memory
-
String — Default:
"9G"
The memory required to run the programs - SVcalling.renameSample.timeMinutes
-
Int — Default:
1 + ceil((size(inputVcf,"G") * 2))
The maximum amount of time the job will run in minutes. - SVcalling.smoove.memory
-
String — Default:
"15G"
The memory required to run the programs. - SVcalling.smoove.timeMinutes
-
Int — Default:
1440
The maximum duration (in minutes) the tool is allowed to run. - SVcalling.survivor.breakpointDistance
-
Int — Default:
1000
The distance between pairwise breakpoints between SVs - SVcalling.survivor.distanceBySvSize
-
Int — Default:
0
A boolean to predict the pairwise distance between the SVs based on their size - SVcalling.survivor.memory
-
String — Default:
"24G"
The memory required to run the programs - SVcalling.survivor.minSize
-
Int — Default:
30
The mimimum size of SV to be merged - SVcalling.survivor.strandType
-
Int — Default:
1
A boolean to include strand type of an SV to be merged - SVcalling.survivor.suppVecs
-
Int — Default:
2
The minimum number of SV callers to support the merging - SVcalling.survivor.svType
-
Int — Default:
1
A boolean to include the type SV to be merged - SVcalling.survivor.timeMinutes
-
Int — Default:
60
The maximum amount of time the job will run in minutes.
Other inputs
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- SVcalling.delly2vcf.outputType
-
String — Default:
"z"
Output type: v=vcf, z=vcf.gz, b=bcf, u=uncompressed bcf