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Inputs for PairedCnvCalling
The following is an overview of all available inputs in PairedCnvCalling.
Required inputs
- PairedCnvCalling.caseBam
-
File
The BAM file for the case sample. - PairedCnvCalling.caseBamIndex
-
File
The index for the case sample's BAM file. - PairedCnvCalling.caseSampleName
-
String
The name of the case sample. - PairedCnvCalling.commonVariantSites
-
File
Interval list or VCF file of common variant sites (to retrieve the allelic counts for). Preferably a list variants from the sample being analysed. For targeted/exome sequencing the list should be limited to variants within the sequenced regions, due to memory usage. - PairedCnvCalling.controlBam
-
File
The BAM file for the control sample. - PairedCnvCalling.controlBamIndex
-
File
The index for the control sample's BAM file. - PairedCnvCalling.controlSampleName
-
String
The name of the control sample. - PairedCnvCalling.preprocessedIntervals
-
File
Intervals to operate on. Should be produced by gatk PreprocessIntervals (eg. using CNV-PON.wdl). - PairedCnvCalling.referenceFasta
-
File
The reference fasta file. - PairedCnvCalling.referenceFastaDict
-
File
The sequence dictionary associated with the reference fasta file. - PairedCnvCalling.referenceFastaFai
-
File
The index for the reference fasta file.
Other common inputs
- PairedCnvCalling.annotatedIntervals
-
File?
An annotated set of intervals as generated by AnnotateIntervals (eg. using CNV-PON.wdl). Will be ignored if PON is provided. - PairedCnvCalling.commonVariantSitesIndex
-
File?
The index for commonVariantSitesIndex. - PairedCnvCalling.outputDir
-
String — Default:
"."
The directory the output should be written to. - PairedCnvCalling.PON
-
File?
A read counts panel of normals as generated by gatk CreateReadCountPanelOfNormals (eg. using CNV-PON.wdl).
Advanced inputs
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- PairedCnvCalling.caseSample.callCopyRatioSegments.javaXmx
-
String — Default:
"2G"
The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead. - PairedCnvCalling.caseSample.callCopyRatioSegments.memory
-
String — Default:
"3G"
The amount of memory this job will use. - PairedCnvCalling.caseSample.callCopyRatioSegments.timeMinutes
-
Int — Default:
2
The maximum amount of time the job will run in minutes. - PairedCnvCalling.caseSample.collectAllelicCounts.javaXmx
-
String — Default:
"10G"
The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead. - PairedCnvCalling.caseSample.collectAllelicCounts.memory
-
String — Default:
"11G"
The amount of memory this job will use. - PairedCnvCalling.caseSample.collectAllelicCounts.timeMinutes
-
Int — Default:
120
The maximum amount of time the job will run in minutes. - PairedCnvCalling.caseSample.collectReadCounts.intervalMergingRule
-
String — Default:
"OVERLAPPING_ONLY"
Equivalent to gatk CollectReadCounts' `--interval-merging-rule` option. - PairedCnvCalling.caseSample.collectReadCounts.javaXmx
-
String — Default:
"7G"
The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead. - PairedCnvCalling.caseSample.collectReadCounts.memory
-
String — Default:
"8G"
The amount of memory this job will use. - PairedCnvCalling.caseSample.collectReadCounts.timeMinutes
-
Int — Default:
1 + ceil((size(inputBam,"G") * 5))
The maximum amount of time the job will run in minutes. - PairedCnvCalling.caseSample.denoiseReadCounts.javaXmx
-
String — Default:
"4G"
The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead. - PairedCnvCalling.caseSample.denoiseReadCounts.memory
-
String — Default:
"5G"
The amount of memory this job will use. - PairedCnvCalling.caseSample.denoiseReadCounts.timeMinutes
-
Int — Default:
5
The maximum amount of time the job will run in minutes. - PairedCnvCalling.caseSample.modelSegments.javaXmx
-
String — Default:
"10G"
The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead. - PairedCnvCalling.caseSample.modelSegments.maximumNumberOfSmoothingIterations
-
Int — Default:
10
Equivalent to gatk ModelSeqments' `--maximum-number-of-smoothing-iterations` option. - PairedCnvCalling.caseSample.modelSegments.memory
-
String — Default:
"11G"
The amount of memory this job will use. - PairedCnvCalling.caseSample.modelSegments.minimumTotalAlleleCountCase
-
Int — Default:
if defined(normalAllelicCounts) then 0 else 30
Equivalent to gatk ModelSeqments' `--minimum-total-allele-count-case` option. - PairedCnvCalling.caseSample.modelSegments.timeMinutes
-
Int — Default:
60
The maximum amount of time the job will run in minutes. - PairedCnvCalling.caseSample.plotDenoisedCopyRatios.javaXmx
-
String — Default:
"3G"
The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead. - PairedCnvCalling.caseSample.plotDenoisedCopyRatios.memory
-
String — Default:
"4G"
The amount of memory this job will use. - PairedCnvCalling.caseSample.plotDenoisedCopyRatios.timeMinutes
-
Int — Default:
2
The maximum amount of time the job will run in minutes. - PairedCnvCalling.caseSample.plotModeledSegments.javaXmx
-
String — Default:
"3G"
The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead. - PairedCnvCalling.caseSample.plotModeledSegments.memory
-
String — Default:
"4G"
The amount of memory this job will use. - PairedCnvCalling.caseSample.plotModeledSegments.timeMinutes
-
Int — Default:
2
The maximum amount of time the job will run in minutes. - PairedCnvCalling.controlSample.callCopyRatioSegments.javaXmx
-
String — Default:
"2G"
The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead. - PairedCnvCalling.controlSample.callCopyRatioSegments.memory
-
String — Default:
"3G"
The amount of memory this job will use. - PairedCnvCalling.controlSample.callCopyRatioSegments.timeMinutes
-
Int — Default:
2
The maximum amount of time the job will run in minutes. - PairedCnvCalling.controlSample.collectAllelicCounts.javaXmx
-
String — Default:
"10G"
The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead. - PairedCnvCalling.controlSample.collectAllelicCounts.memory
-
String — Default:
"11G"
The amount of memory this job will use. - PairedCnvCalling.controlSample.collectAllelicCounts.timeMinutes
-
Int — Default:
120
The maximum amount of time the job will run in minutes. - PairedCnvCalling.controlSample.collectReadCounts.intervalMergingRule
-
String — Default:
"OVERLAPPING_ONLY"
Equivalent to gatk CollectReadCounts' `--interval-merging-rule` option. - PairedCnvCalling.controlSample.collectReadCounts.javaXmx
-
String — Default:
"7G"
The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead. - PairedCnvCalling.controlSample.collectReadCounts.memory
-
String — Default:
"8G"
The amount of memory this job will use. - PairedCnvCalling.controlSample.collectReadCounts.timeMinutes
-
Int — Default:
1 + ceil((size(inputBam,"G") * 5))
The maximum amount of time the job will run in minutes. - PairedCnvCalling.controlSample.denoiseReadCounts.javaXmx
-
String — Default:
"4G"
The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead. - PairedCnvCalling.controlSample.denoiseReadCounts.memory
-
String — Default:
"5G"
The amount of memory this job will use. - PairedCnvCalling.controlSample.denoiseReadCounts.timeMinutes
-
Int — Default:
5
The maximum amount of time the job will run in minutes. - PairedCnvCalling.controlSample.modelSegments.javaXmx
-
String — Default:
"10G"
The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead. - PairedCnvCalling.controlSample.modelSegments.maximumNumberOfSmoothingIterations
-
Int — Default:
10
Equivalent to gatk ModelSeqments' `--maximum-number-of-smoothing-iterations` option. - PairedCnvCalling.controlSample.modelSegments.memory
-
String — Default:
"11G"
The amount of memory this job will use. - PairedCnvCalling.controlSample.modelSegments.minimumTotalAlleleCountCase
-
Int — Default:
if defined(normalAllelicCounts) then 0 else 30
Equivalent to gatk ModelSeqments' `--minimum-total-allele-count-case` option. - PairedCnvCalling.controlSample.modelSegments.timeMinutes
-
Int — Default:
60
The maximum amount of time the job will run in minutes. - PairedCnvCalling.controlSample.plotDenoisedCopyRatios.javaXmx
-
String — Default:
"3G"
The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead. - PairedCnvCalling.controlSample.plotDenoisedCopyRatios.memory
-
String — Default:
"4G"
The amount of memory this job will use. - PairedCnvCalling.controlSample.plotDenoisedCopyRatios.timeMinutes
-
Int — Default:
2
The maximum amount of time the job will run in minutes. - PairedCnvCalling.controlSample.plotModeledSegments.javaXmx
-
String — Default:
"3G"
The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead. - PairedCnvCalling.controlSample.plotModeledSegments.memory
-
String — Default:
"4G"
The amount of memory this job will use. - PairedCnvCalling.controlSample.plotModeledSegments.timeMinutes
-
Int — Default:
2
The maximum amount of time the job will run in minutes. - PairedCnvCalling.dockerImages
-
Map[String,String] — Default:
{"gatk": "broadinstitute/gatk:4.1.8.0"}
The docker images used. Changing this may result in errors which the developers may choose not to address. - PairedCnvCalling.minimumContigLength
-
Int?
The minimum length for a contig to be included in the plots.
Do not set these inputs!
The following inputs should not be set, even though womtool may show them as being available inputs.
- PairedCnvCalling.controlSample.matchedNormalAllelicCounts