Inputs for SomaticSvCalling
The following is an overview of all available inputs in SomaticSvCalling.
Required inputs
- SomaticSvCalling.bwaIndex
-
BwaIndex
The BWA index for the reference genome. - SomaticSvCalling.normalBamIndexes
-
Array[File]
The indexes for the normal BAM files in the same order as the BAM files. - SomaticSvCalling.normalBams
-
Array[File]
The BAM files for the normal samples in the same order as IDs. - SomaticSvCalling.normalIds
-
Array[String]
The IDs of the normal samples in the same order as the BAM files. - SomaticSvCalling.pairs
-
Array[Pair[String,String]]
The tumor-normal pairs. The left element is the ID for the tumor and the right element is the ID for the associated normal. - SomaticSvCalling.referenceFasta
-
File
The FASTA file for the reference genome. - SomaticSvCalling.referenceFastaFai
-
File
The index for the reference genomes FASTA file. - SomaticSvCalling.tumorBamIndexes
-
Array[File]
The indexes for the tumor BAM files in the same order as the BAM files. - SomaticSvCalling.tumorBams
-
Array[File]
The BAM files for the tumor samples in the same order as IDs. - SomaticSvCalling.tumorIds
-
Array[String]
The IDs of the tumor samples in the same order as the BAM files.
Other common inputs
- SomaticSvCalling.gridssPonBed
-
File?
A premade PON single breakend BED file for GRIDSS. - SomaticSvCalling.gridssPonBedpe
-
File?
A premade PON breakpoint BEDPE file for GRIDSS. - SomaticSvCalling.mantaSomatic.callRegions
-
File?
The bed file which indicates the regions to operate on. - SomaticSvCalling.mantaSomatic.callRegionsIndex
-
File?
The index of the bed file which indicates the regions to operate on. - SomaticSvCalling.mantaSomatic.exome
-
Boolean — Default:
false
Whether or not the data is from exome sequencing. - SomaticSvCalling.outputDir
-
String — Default:
"."
The directory the output should be written to.
Advanced inputs
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- SomaticSvCalling.dellyBcfToVcf.dockerImage
-
String — Default:
"quay.io/biocontainers/bcftools:1.10.2--h4f4756c_2"
The docker image used for this task. Changing this may result in errors which the developers may choose not to address. - SomaticSvCalling.dellyBcfToVcf.exclude
-
String?
Exclude sites for which the expression is true (see man page for details). - SomaticSvCalling.dellyBcfToVcf.excludeUncalled
-
Boolean — Default:
false
Exclude sites without a called genotype (see man page for details). - SomaticSvCalling.dellyBcfToVcf.include
-
String?
Select sites for which the expression is true (see man page for details). - SomaticSvCalling.dellyBcfToVcf.memory
-
String — Default:
"256MiB"
The amount of memory this job will use. - SomaticSvCalling.dellyBcfToVcf.samples
-
Array[String] — Default:
[]
A list of sample names to include. - SomaticSvCalling.dellyBcfToVcf.timeMinutes
-
Int — Default:
1 + ceil(size(inputFile,"G"))
The maximum amount of time the job will run in minutes. - SomaticSvCalling.dellyCall.dockerImage
-
String — Default:
"quay.io/biocontainers/delly:1.1.6--ha41ced6_0"
The docker image used for this task. Changing this may result in errors which the developers may choose not to address. - SomaticSvCalling.dellyCall.genotypeBcf
-
File?
A BCF with SVs to get genotyped in the samples. - SomaticSvCalling.dellyCall.genotypeBcfIndex
-
File?
The index for the genotype BCF file. - SomaticSvCalling.dellyCall.memory
-
String — Default:
"15GiB"
The memory required to run the programs. - SomaticSvCalling.dellyCall.timeMinutes
-
Int — Default:
600
The maximum amount of time the job will run in minutes. - SomaticSvCalling.dellyGenotypeNormals.dockerImage
-
String — Default:
"quay.io/biocontainers/delly:1.1.6--ha41ced6_0"
The docker image used for this task. Changing this may result in errors which the developers may choose not to address. - SomaticSvCalling.dellyGenotypeNormals.memory
-
String — Default:
"15GiB"
The memory required to run the programs. - SomaticSvCalling.dellyGenotypeNormals.timeMinutes
-
Int — Default:
600
The maximum amount of time the job will run in minutes. - SomaticSvCalling.dellyPonFilter.dockerImage
-
String — Default:
"quay.io/biocontainers/delly:1.1.6--ha41ced6_0"
The docker image used for this task. Changing this may result in errors which the developers may choose not to address. - SomaticSvCalling.dellyPonFilter.memory
-
String — Default:
"15GiB"
The memory required to run the programs. - SomaticSvCalling.dellyPonFilter.timeMinutes
-
Int — Default:
300
The maximum amount of time the job will run in minutes. - SomaticSvCalling.dellySomaticFilter.dockerImage
-
String — Default:
"quay.io/biocontainers/delly:1.1.6--ha41ced6_0"
The docker image used for this task. Changing this may result in errors which the developers may choose not to address. - SomaticSvCalling.dellySomaticFilter.memory
-
String — Default:
"15GiB"
The memory required to run the programs. - SomaticSvCalling.dellySomaticFilter.timeMinutes
-
Int — Default:
300
The maximum amount of time the job will run in minutes. - SomaticSvCalling.filterGridssPon.dockerImage
-
String — Default:
"quay.io/biowdl/gridss:2.12.2"
The docker image used for this task. Changing this may result in errors which the developers may choose not to address. - SomaticSvCalling.filterGridssPon.memory
-
String — Default:
"1GiB"
The amount of memory this job will use. - SomaticSvCalling.filterGridssPon.minimumScore
-
Int — Default:
3
The minimum number normal samples an SV must have been found in to be kept. - SomaticSvCalling.filterGridssPon.timeMinutes
-
Int — Default:
20
The maximum amount of time the job will run in minutes. - SomaticSvCalling.generateGridssPon.dockerImage
-
String — Default:
"quay.io/biowdl/gridss:2.12.2"
The docker image used for this task. Changing this may result in errors which the developers may choose not to address. - SomaticSvCalling.generateGridssPon.javaXmx
-
String — Default:
"8G"
The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead. - SomaticSvCalling.generateGridssPon.memory
-
String — Default:
"9GiB"
The amount of memory this job will use. - SomaticSvCalling.generateGridssPon.threads
-
Int — Default:
8
The number of the threads to use. - SomaticSvCalling.generateGridssPon.timeMinutes
-
Int — Default:
120
The maximum amount of time the job will run in minutes. - SomaticSvCalling.gridssSeparateSamples.dockerImage
-
String — Default:
"quay.io/biocontainers/bcftools:1.10.2--h4f4756c_2"
The docker image used for this task. Changing this may result in errors which the developers may choose not to address. - SomaticSvCalling.gridssSeparateSamples.exclude
-
String?
Exclude sites for which the expression is true (see man page for details). - SomaticSvCalling.gridssSeparateSamples.excludeUncalled
-
Boolean — Default:
false
Exclude sites without a called genotype (see man page for details). - SomaticSvCalling.gridssSeparateSamples.include
-
String?
Select sites for which the expression is true (see man page for details). - SomaticSvCalling.gridssSeparateSamples.memory
-
String — Default:
"256MiB"
The amount of memory this job will use. - SomaticSvCalling.gridssSeparateSamples.timeMinutes
-
Int — Default:
1 + ceil(size(inputFile,"G"))
The maximum amount of time the job will run in minutes. - SomaticSvCalling.gridssSomaticFilter.dockerImage
-
String — Default:
"quay.io/biowdl/gridss:2.12.2"
The docker image used for this task. Changing this may result in errors which the developers may choose not to address. - SomaticSvCalling.gridssSomaticFilter.memory
-
String — Default:
"16GiB"
The amount of memory this job will use. - SomaticSvCalling.gridssSomaticFilter.timeMinutes
-
Int — Default:
60
The maximum amount of time the job will run in minutes. - SomaticSvCalling.gridssSvTyped.dockerImage
-
String — Default:
"quay.io/biocontainers/bioconductor-structuralvariantannotation:1.10.0--r41hdfd78af_0"
The docker image used for this task. Changing this may result in errors which the developers may choose not to address. - SomaticSvCalling.gridssSvTyped.memory
-
String — Default:
"32GiB"
The amount of memory this job will use. - SomaticSvCalling.gridssSvTyped.timeMinutes
-
Int — Default:
240
The maximum amount of time the job will run in minutes. - SomaticSvCalling.groupedGridss.blacklistBed
-
File?
A bed file with blaclisted regins. - SomaticSvCalling.groupedGridss.dockerImage
-
String — Default:
"quay.io/biowdl/gridss:2.12.2"
The docker image used for this task. Changing this may result in errors which the developers may choose not to address. - SomaticSvCalling.groupedGridss.gridssProperties
-
File?
A properties file for gridss. - SomaticSvCalling.groupedGridss.jvmHeapSizeGb
-
Int — Default:
64
The size of JVM heap for assembly and variant calling - SomaticSvCalling.groupedGridss.nonJvmMemoryGb
-
Int — Default:
10
The amount of memory in Gb to be requested besides JVM memory. - SomaticSvCalling.groupedGridss.threads
-
Int — Default:
12
The number of the threads to use. - SomaticSvCalling.groupedGridss.timeMinutes
-
Int — Default:
ceil((7200 / threads)) + 1800
The maximum amount of time the job will run in minutes. - SomaticSvCalling.mantaSomatic.cores
-
Int — Default:
1
The number of cores to use. - SomaticSvCalling.mantaSomatic.dockerImage
-
String — Default:
"quay.io/biocontainers/manta:1.4.0--py27_1"
The docker image used for this task. Changing this may result in errors which the developers may choose not to address. - SomaticSvCalling.mantaSomatic.memoryGb
-
Int — Default:
4
The amount of memory this job will use in Gigabytes. - SomaticSvCalling.mantaSomatic.timeMinutes
-
Int — Default:
2880
The maximum amount of time the job will run in minutes. - SomaticSvCalling.normalPosition.dockerImage
-
String — Default:
"python@sha256:e0f6a4df17d5707637fa3557ab266f44dddc46ebfc82b0f1dbe725103961da4e"
The docker image used for this task. Changing this may result in errors which the developers may choose not to address. - SomaticSvCalling.normalPositionGridss.dockerImage
-
String — Default:
"python@sha256:e0f6a4df17d5707637fa3557ab266f44dddc46ebfc82b0f1dbe725103961da4e"
The docker image used for this task. Changing this may result in errors which the developers may choose not to address. - SomaticSvCalling.tumorPosition.dockerImage
-
String — Default:
"python@sha256:e0f6a4df17d5707637fa3557ab266f44dddc46ebfc82b0f1dbe725103961da4e"
The docker image used for this task. Changing this may result in errors which the developers may choose not to address. - SomaticSvCalling.tumorPositionGridss.dockerImage
-
String — Default:
"python@sha256:e0f6a4df17d5707637fa3557ab266f44dddc46ebfc82b0f1dbe725103961da4e"
The docker image used for this task. Changing this may result in errors which the developers may choose not to address.