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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.annotateDH.memory

String — Default: "15G"
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: "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.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: "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", "duphold": "quay.io/biocontainers/duphold:0.2.1--h516909a_1"}
A map describing the docker image used for the tasks.

SVcalling.excludeFpDupDel

Boolean — Default: false
Option to exclude false positive duplications and deletions according to DUPHOLD.

SVcalling.excludeMisHomRef

Boolean — Default: false
Option to exclude missing and homozygous reference genotypes.

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.newId

String — Default: "\'%CHROM\\_%POS\'"
Assign ID on the fly (e.g. --set-id +'%CHROM\_%POS').

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: "256M"
The amount of memory this job will use.

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: "256M"
The amount of memory this job will use.

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: "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.setId.annsFile

File?
Bgzip-compressed and tabix-indexed file with annotations (see man page for details).

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: "256M"
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: 1 + ceil(size(inputFile,"G"))
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.sort.memory

String — Default: "256M"
The amount of memory this job will use.

SVcalling.sort.timeMinutes

Int — Default: 1 + ceil(size(inputFile,"G"))
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: "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

Boolean — Default: true
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

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.