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
-
BwaIndex
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. - SVcalling.setId.annsFile
-
File?
Bgzip-compressed and tabix-indexed file with annotations (see man page for details). - SVcalling.setId.annsFileIndex
-
File?
The index for annsFile. - SVcalling.setId.inputFileIndex
-
File?
The index for the input vcf or bcf.
Advanced inputs
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- SVcalling.annotateDH.memory
-
String — Default:
"15GiB"
The memory required to run the programs. - SVcalling.annotateDH.timeMinutes
-
Int — Default:
1440
The maximum duration (in minutes) the tool is allowed to run. - SVcalling.clever.memory
-
String — Default:
"80GiB"
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:
2200
The maximum amount of time the job will run in minutes. - SVcalling.delly.genotypeBcf
-
File?
A BCF with SVs to get genotyped in the samples. - SVcalling.delly.genotypeBcfIndex
-
File?
The index for the genotype BCF file. - SVcalling.delly.memory
-
String — Default:
"15GiB"
The memory required to run the programs. - SVcalling.delly.timeMinutes
-
Int — Default:
600
The maximum amount of time the job will run in minutes. - SVcalling.delly2vcf.exclude
-
String?
Exclude sites for which the expression is true (see man page for details). - SVcalling.delly2vcf.excludeUncalled
-
Boolean — Default:
false
Exclude sites without a called genotype (see man page for details). - SVcalling.delly2vcf.include
-
String?
Select sites for which the expression is true (see man page for details). - SVcalling.delly2vcf.memory
-
String — Default:
"256MiB"
The amount of memory this job will use. - SVcalling.delly2vcf.samples
-
Array[String] — Default:
[]
A list of sample names to include. - 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/biowdl/clever-toolkit:2.4", "delly": "quay.io/biocontainers/delly:0.8.5--hf3ca161_0", "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:1.0.7--hd03093a_2", "smoove": "quay.io/biocontainers/smoove:0.2.5--0", "duphold": "quay.io/biocontainers/duphold:0.2.1--h516909a_1", "gridss": "quay.io/biowdl/gridss:2.12.2"}
A map describing the docker image used for the tasks. - SVcalling.excludeMisHomRef
-
Boolean — Default:
false
Option to exclude missing and homozygous reference genotypes. - SVcalling.FilterShortReadsBam.memory
-
String — Default:
"1GiB"
The amount of memory this job will use. - SVcalling.FilterShortReadsBam.timeMinutes
-
Int — Default:
1 + ceil((size(bamFile,"GiB") * 8))
The maximum amount of time the job will run in minutes. - SVcalling.getIntersections.excludeUncalled
-
Boolean — Default:
false
Exclude sites without a called genotype (see man page for details). - SVcalling.getIntersections.include
-
String?
Select sites for which the expression is true (see man page for details). - SVcalling.getIntersections.memory
-
String — Default:
"256MiB"
The amount of memory this job will use. - SVcalling.getIntersections.samples
-
Array[String] — Default:
[]
A list of sample names to include. - SVcalling.getIntersections.timeMinutes
-
Int — Default:
1 + ceil(size(inputFile,"G"))
The maximum amount of time the job will run in minutes. - SVcalling.getSVtype.exclude
-
String?
Exclude sites for which the expression is true (see man page for details). - SVcalling.getSVtype.excludeUncalled
-
Boolean — Default:
false
Exclude sites without a called genotype (see man page for details). - SVcalling.getSVtype.memory
-
String — Default:
"256MiB"
The amount of memory this job will use. - SVcalling.getSVtype.samples
-
Array[String] — Default:
[]
A list of sample names to include. - SVcalling.getSVtype.timeMinutes
-
Int — Default:
1 + ceil(size(inputFile,"G"))
The maximum amount of time the job will run in minutes. - SVcalling.gridss.blacklistBed
-
File?
A bed file with blaclisted regins. - SVcalling.gridss.gridssProperties
-
File?
A properties file for gridss. - SVcalling.gridss.jvmHeapSizeGb
-
Int — Default:
64
The size of JVM heap for assembly and variant calling - SVcalling.gridss.nonJvmMemoryGb
-
Int — Default:
10
The amount of memory in Gb to be requested besides JVM memory. - SVcalling.gridss.normalBai
-
File?
The index for normalBam. - SVcalling.gridss.normalBam
-
File?
The BAM file for the normal/control sample. - SVcalling.gridss.normalLabel
-
String?
The name of the normal sample. - SVcalling.gridss.threads
-
Int — Default:
12
The number of the threads to use. - SVcalling.gridss.timeMinutes
-
Int — Default:
ceil((7200 / threads)) + 1800
The maximum amount of time the job will run in minutes. - SVcalling.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. - SVcalling.gridssSvTyped.memory
-
String — Default:
"32GiB"
The amount of memory this job will use. - SVcalling.gridssSvTyped.timeMinutes
-
Int — Default:
240
The maximum amount of time the job will run in minutes. - SVcalling.manta.timeMinutes
-
Int — Default:
2880
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:
"250GiB"
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:
2880
The maximum amount of time the job will run in minutes. - SVcalling.removeFpDupDel.exclude
-
String?
Exclude sites for which the expression is true (see man page for details). - SVcalling.removeFpDupDel.excludeUncalled
-
Boolean — Default:
false
Exclude sites without a called genotype (see man page for details). - SVcalling.removeFpDupDel.memory
-
String — Default:
"256MiB"
The amount of memory this job will use. - SVcalling.removeFpDupDel.samples
-
Array[String] — Default:
[]
A list of sample names to include. - SVcalling.removeFpDupDel.timeMinutes
-
Int — Default:
1 + ceil(size(inputFile,"G"))
The maximum amount of time the job will run in minutes. - SVcalling.removeMisHomRR.include
-
String?
Select sites for which the expression is true (see man page for details). - SVcalling.removeMisHomRR.memory
-
String — Default:
"256MiB"
The amount of memory this job will use. - SVcalling.removeMisHomRR.samples
-
Array[String] — Default:
[]
A list of sample names to include. - SVcalling.removeMisHomRR.timeMinutes
-
Int — Default:
1 + ceil(size(inputFile,"G"))
The maximum amount of time the job will run in minutes. - SVcalling.renameSample.javaXmx
-
String — Default:
"8G"
The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead. - SVcalling.renameSample.memory
-
String — Default:
"9GiB"
The memory required to run the programs. - SVcalling.renameSample.timeMinutes
-
Int — Default:
1 + ceil((size(inputVcf,"GiB") * 2))
The maximum amount of time the job will run in minutes. - SVcalling.runClever
-
Boolean — Default:
false
Whether or not to run clever. - SVcalling.runDupHold
-
Boolean — Default:
false
Option to run duphold annotation and filter FP deletions and duplications. - SVcalling.runSmoove
-
Boolean — Default:
true
Whether or not to run smoove. - SVcalling.setId.collapse
-
String?
Treat as identical records with <snps|indels|both|all|some|none>, see man page for details. - SVcalling.setId.columns
-
Array[String] — Default:
[]
Comma-separated list of columns or tags to carry over from the annotation file (see man page for details). - SVcalling.setId.exclude
-
String?
Exclude sites for which the expression is true (see man page for details). - SVcalling.setId.force
-
Boolean — Default:
false
Continue even when parsing errors, such as undefined tags, are encountered. - SVcalling.setId.headerLines
-
File?
Lines to append to the VCF header (see man page for details). - SVcalling.setId.include
-
String?
Select sites for which the expression is true (see man page for details). - SVcalling.setId.keepSites
-
Boolean — Default:
false
Keep sites which do not pass -i and -e expressions instead of discarding them. - SVcalling.setId.markSites
-
String?
Annotate sites which are present ('+') or absent ('-') in the -a file with a new INFO/TAG flag. - SVcalling.setId.memory
-
String — Default:
"4GiB"
The amount of memory this job will use. - SVcalling.setId.noVersion
-
Boolean — Default:
false
Do not append version and command line information to the output VCF header. - SVcalling.setId.regions
-
String?
Restrict to comma-separated list of regions. - SVcalling.setId.regionsFile
-
File?
Restrict to regions listed in a file. - SVcalling.setId.removeAnns
-
Array[String] — Default:
[]
List of annotations to remove (see man page for details). - SVcalling.setId.renameChrs
-
File?
rename chromosomes according to the map in file (see man page for details). - SVcalling.setId.samples
-
Array[String] — Default:
[]
List of samples for sample stats, "-" to include all samples. - SVcalling.setId.samplesFile
-
File?
File of samples to include. - SVcalling.setId.singleOverlaps
-
Boolean — Default:
false
keep memory requirements low with very large annotation files. - SVcalling.setId.threads
-
Int — Default:
0
Number of extra decompression threads [0]. - SVcalling.setId.timeMinutes
-
Int — Default:
60 + ceil(size(inputFile,"G"))
The maximum amount of time the job will run in minutes. - SVcalling.smoove.memory
-
String — Default:
"15GiB"
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.sort.memory
-
String — Default:
"5GiB"
The amount of memory this job will use. - SVcalling.sort.timeMinutes
-
Int — Default:
1 + ceil(size(inputFile,"G")) * 5
The maximum amount of time the job will run in minutes. - SVcalling.survivor.breakpointDistance
-
Int — Default:
1000
The distance between pairwise breakpoints between SVs. - SVcalling.survivor.distanceBySvSize
-
Boolean — Default:
false
A boolean to predict the pairwise distance between the SVs based on their size. - SVcalling.survivor.memory
-
String — Default:
"24GiB"
The memory required to run the programs. - SVcalling.survivor.minSize
-
Int — Default:
30
The mimimum size of SV to be merged. - SVcalling.survivor.strandType
-
Boolean — Default:
true
A boolean to include strand type of an SV to be merged. - SVcalling.survivor.svType
-
Boolean — Default:
true
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. - SVcalling.svtypes
-
Array[String] — Default:
["DEL", "DUP", "INS", "INV", "BND"]
List of svtypes to be further processed and output by the pipeline.