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Inputs for PanelOfNormals
The following is an overview of all available inputs in PanelOfNormals.
Required inputs
- PanelOfNormals.referenceFasta
-
File
The reference fasta file. - PanelOfNormals.referenceFastaDict
-
File
The sequence dictionary associated with the reference fasta file. - PanelOfNormals.referenceFastaFai
-
File
The index for the reference fasta file.
Other common inputs
- PanelOfNormals.annotateIntervals.mappabilityTrack
-
File?
Equivalent to gatk AnnotateIntervals' `--mappability-track` option. - PanelOfNormals.annotateIntervals.segmentalDuplicationTrack
-
File?
Equivalent to gatk AnnotateIntervals' `--segmenta-duplicarion-track` option. - PanelOfNormals.inputBamIndexes
-
Array[File] — Default:
[]
The indexes for the input BAM files. - PanelOfNormals.inputBams
-
Array[File] — Default:
[]
The BAM files for the samples to include in the PON. May be empty so just the annotated intervals can be created. - PanelOfNormals.outputDir
-
String — Default:
"."
The directory the output should be written to. - PanelOfNormals.PONname
-
String — Default:
"PON"
The name the PON file should be given. - PanelOfNormals.regions
-
File?
The regions to operate on.
Advanced inputs
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- PanelOfNormals.annotateIntervals.featureQueryLookahead
-
Int — Default:
1000000
Equivalent to gatk AnnotateIntervals' `--feature-query-lookahead` option. - PanelOfNormals.annotateIntervals.intervalMergingRule
-
String — Default:
"OVERLAPPING_ONLY"
Equivalent to gatk AnnotateIntervals' `--interval-merging-rule` option. - PanelOfNormals.annotateIntervals.javaXmx
-
String — Default:
"2G"
The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead. - PanelOfNormals.annotateIntervals.memory
-
String — Default:
"3GiB"
The amount of memory this job will use. - PanelOfNormals.annotateIntervals.timeMinutes
-
Int — Default:
5
The maximum amount of time the job will run in minutes. - PanelOfNormals.collectReadCounts.intervalMergingRule
-
String — Default:
"OVERLAPPING_ONLY"
Equivalent to gatk CollectReadCounts' `--interval-merging-rule` option. - PanelOfNormals.collectReadCounts.javaXmx
-
String — Default:
"7G"
The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead. - PanelOfNormals.collectReadCounts.memory
-
String — Default:
"8GiB"
The amount of memory this job will use. - PanelOfNormals.collectReadCounts.timeMinutes
-
Int — Default:
1 + ceil((size(inputBam,"G") * 5))
The maximum amount of time the job will run in minutes. - PanelOfNormals.createReadCountPanelOfNormals.javaXmx
-
String — Default:
"7G"
The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead. - PanelOfNormals.createReadCountPanelOfNormals.memory
-
String — Default:
"8GiB"
The amount of memory this job will use. - PanelOfNormals.createReadCountPanelOfNormals.timeMinutes
-
Int — Default:
5
The maximum amount of time the job will run in minutes. - PanelOfNormals.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. - PanelOfNormals.performExplicitGcCorrection
-
Boolean — Default:
true
Whether or not explicit GC correction should be used for PON generation. Setting this to false will also disable the creation of annotated intervals. - PanelOfNormals.preprocessIntervals.binLength
-
Int — Default:
if defined(intervals) then 0 else 1000
The size of the bins to be created. Should be 0 for targeted/exome sequencing. - PanelOfNormals.preprocessIntervals.intervalMergingRule
-
String — Default:
"OVERLAPPING_ONLY"
Equivalent to gatk PreprocessIntervals' `--interval-merging-rule` option. - PanelOfNormals.preprocessIntervals.javaXmx
-
String — Default:
"3G"
The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead. - PanelOfNormals.preprocessIntervals.memory
-
String — Default:
"4GiB"
The amount of memory this job will use. - PanelOfNormals.preprocessIntervals.padding
-
Int — Default:
if defined(intervals) then 250 else 0
The padding to be added to the bins. Should be 0 if contiguos binning is used, eg with WGS. - PanelOfNormals.preprocessIntervals.timeMinutes
-
Int — Default:
1 + ceil((size(referenceFasta,"G") * 6))
The maximum amount of time the job will run in minutes.