GatkMutect2¶
Gatk4Mutect2 · 1 contributor · 7 versions
USAGE: Mutect2 [arguments] Call somatic SNVs and indels via local assembly of haplotypes Version:4.1.2.0
Quickstart¶
from janis_bioinformatics.tools.gatk4.mutect2.versions import GatkMutect2_4_1_8 wf = WorkflowBuilder("myworkflow") wf.step( "gatk4mutect2_step", GatkMutect2_4_1_8( tumorBams=None, reference=None, ) ) wf.output("out", source=gatk4mutect2_step.out) wf.output("stats", source=gatk4mutect2_step.stats) wf.output("f1f2r_out", source=gatk4mutect2_step.f1f2r_out) wf.output("bam", source=gatk4mutect2_step.bam)
OR
- Install Janis
- Ensure Janis is configured to work with Docker or Singularity.
- Ensure all reference files are available:
Note
More information about these inputs are available below.
- Generate user input files for Gatk4Mutect2:
# user inputs
janis inputs Gatk4Mutect2 > inputs.yaml
inputs.yaml
reference: reference.fasta
tumorBams:
- tumorBams_0.bam
- tumorBams_1.bam
- Run Gatk4Mutect2 with:
janis run [...run options] \
--inputs inputs.yaml \
Gatk4Mutect2
Information¶
| ID: | Gatk4Mutect2 |
|---|---|
| URL: | https://software.broadinstitute.org/gatk/documentation/tooldocs/4.0.10.0/org_broadinstitute_hellbender_tools_walkers_mutect_Mutect2.php |
| Versions: | 4.1.8.1, 4.1.7.0, 4.1.6.0, 4.1.4.0, 4.1.3.0, 4.1.2.0, 4.0.12.0 |
| Container: | broadinstitute/gatk:4.1.8.1 |
| Authors: | Michael Franklin |
| Citations: | See https://software.broadinstitute.org/gatk/documentation/article?id=11027 for more information |
| Created: | 2018-12-24 |
| Updated: | 2019-01-24 |
Outputs¶
| name | type | documentation |
|---|---|---|
| out | Gzipped<VCF> | To determine type |
| stats | TextFile | To determine type |
| f1f2r_out | CompressedTarFile | To determine type |
| bam | Optional<IndexedBam> | File to which assembled haplotypes should be written |
Additional configuration (inputs)¶
| name | type | prefix | position | documentation |
|---|---|---|---|---|
| tumorBams | Array<IndexedBam> | -I | (–input) BAM/SAM/CRAM file containing reads This argument must be specified at least once. Required. | |
| reference | FastaWithIndexes | –reference | (-R) Reference sequence file Required. | |
| javaOptions | Optional<Array<String>> | |||
| compression_level | Optional<Integer> | Compression level for all compressed files created (e.g. BAM and VCF). Default value: 2. | ||
| normalBams | Optional<Array<IndexedBam>> | -I | (–input) Extra BAM/SAM/CRAM file containing reads This argument must be specified at least once. Required. | |
| normalSample | Optional<String> | –normal-sample | (–normal-sample, if) May be URL-encoded as output by GetSampleName with | |
| outputPrefix | Optional<String> | Used as a prefix for the outputFilename if not specified, with format: {outputPrefix}.vcf.gz | ||
| outputFilename | Optional<Filename> | -O | 20 | |
| outputBamName | Optional<String> | -bamout | File to which assembled haplotypes should be written | |
| activityProfileOut | Optional<String> | –activity-profile-out | Default value: null. | |
| addOutputSamProgramRecord | Optional<Boolean> | -add-output-sam-program-record | (–add-output-sam-program-record) If true, adds a PG tag to created SAM/BAM/CRAM files. Default value: true. Possible values: {true, false} | |
| addOutputVcfCommandLine | Optional<Boolean> | -add-output-vcf-command-line | (–add-output-vcf-command-line) If true, adds a command line header line to created VCF files. Default value: true. Possible values: {true, false} | |
| afOfAllelesNotInResource | Optional<String> | –af-of-alleles-not-in-resource | (-default-af) Population allele fraction assigned to alleles not found in germline resource. Please see docs/mutect/mutect2.pdf fora derivation of the default value. Default value: -1.0. | |
| alleles | Optional<String> | –alleles | The set of alleles for which to force genotyping regardless of evidence Default value: null. | |
| annotation | Optional<String> | –annotation | (-A) One or more specific annotations to add to variant calls This argument may be specified 0 or more times. Default value: null. Possible Values: {AlleleFraction, AS_BaseQualityRankSumTest, AS_FisherStrand, AS_InbreedingCoeff, AS_MappingQualityRankSumTest, AS_QualByDepth, AS_ReadPosRankSumTest, AS_RMSMappingQuality, AS_StrandOddsRatio, BaseQuality, BaseQualityRankSumTest, ChromosomeCounts, ClippingRankSumTest, CountNs, Coverage, DepthPerAlleleBySample, DepthPerSampleHC, ExcessHet, FisherStrand, FragmentLength, GenotypeSummaries, InbreedingCoeff, LikelihoodRankSumTest, MappingQuality, MappingQualityRankSumTest, MappingQualityZero, OrientationBiasReadCounts, OriginalAlignment, PossibleDeNovo, QualByDepth, ReadPosition, ReadPosRankSumTest, ReferenceBases, RMSMappingQuality, SampleList, StrandBiasBySample, StrandOddsRatio, TandemRepeat, UniqueAltReadCount} | |
| annotationGroup | Optional<String> | –annotation-group | (-G) One or more groups of annotations to apply to variant calls This argument may be specified 0 or more times. Default value: null. Possible Values: {AS_StandardAnnotation, ReducibleAnnotation, StandardAnnotation, StandardHCAnnotation, StandardMutectAnnotation} | |
| annotationsToExclude | Optional<String> | –annotations-to-exclude | (-AX) One or more specific annotations to exclude from variant calls This argument may be specified 0 or more times. Default value: null. Possible Values: {BaseQuality, Coverage, DepthPerAlleleBySample, DepthPerSampleHC, FragmentLength, MappingQuality, OrientationBiasReadCounts, ReadPosition, StrandBiasBySample, TandemRepeat} | |
| arguments_file | Optional<File> | –arguments_file | read one or more arguments files and add them to the command line This argument may be specified 0 or more times. Default value: null. | |
| assemblyRegionOut | Optional<String> | –assembly-region-out | Output the assembly region to this IGV formatted file Default value: null. | |
| baseQualityScoreThreshold | Optional<Integer> | –base-quality-score-threshold | Base qualities below this threshold will be reduced to the minimum (6) Default value: 18. | |
| callableDepth | Optional<Integer> | –callable-depth | Minimum depth to be considered callable for Mutect stats. Does not affect genotyping. Default value: 10. | |
| cloudIndexPrefetchBuffer | Optional<Integer> | –cloud-index-prefetch-buffer | (-CIPB) Size of the cloud-only prefetch buffer (in MB; 0 to disable). Defaults to cloudPrefetchBuffer if unset. Default value: -1. | |
| cloudPrefetchBuffer | Optional<Integer> | –cloud-prefetch-buffer | (-CPB) Size of the cloud-only prefetch buffer (in MB; 0 to disable). Default value: 40. | |
| createOutputBamIndex | Optional<Boolean> | –create-output-bam-index | (-OBI) If true, create a BAM/CRAM index when writing a coordinate-sorted BAM/CRAM file. Default value: true. Possible values: {true, false} | |
| createOutputBamMd5 | Optional<Boolean> | –create-output-bam-md5 | (-OBM) If true, create a MD5 digest for any BAM/SAM/CRAM file created Default value: false. Possible values: {true, false} | |
| createOutputVariantIndex | Optional<Boolean> | –create-output-variant-index | (-OVI) If true, create a VCF index when writing a coordinate-sorted VCF file. Default value: true. Possible values: {true, false} | |
| createOutputVariantMd5 | Optional<Boolean> | –create-output-variant-md5 | (-OVM) If true, create a a MD5 digest any VCF file created. Default value: false. Possible values: {true, false} | |
| disableBamIndexCaching | Optional<Boolean> | –disable-bam-index-caching | (-DBIC) If true, don’t cache bam indexes, this will reduce memory requirements but may harm performance if many intervals are specified. Caching is automatically disabled if there are no intervals specified. Default value: false. Possible values: {true, false} | |
| disableReadFilter | Optional<Boolean> | –disable-read-filter | (-DF) Read filters to be disabled before analysis This argument may be specified 0 or more times. Default value: null. Possible Values: {GoodCigarReadFilter, MappedReadFilter, MappingQualityAvailableReadFilter, MappingQualityNotZeroReadFilter, MappingQualityReadFilter, NonChimericOriginalAlignmentReadFilter, NonZeroReferenceLengthAlignmentReadFilter, NotDuplicateReadFilter, NotSecondaryAlignmentReadFilter, PassesVendorQualityCheckReadFilter, ReadLengthReadFilter, WellformedReadFilter} | |
| disableSequenceDictionaryValidation | Optional<Boolean> | -disable-sequence-dictionary-validation | (–disable-sequence-dictionary-validation) If specified, do not check the sequence dictionaries from our inputs for compatibility. Use at your own risk! Default value: false. Possible values: {true, false} | |
| downsamplingStride | Optional<Integer> | –downsampling-stride | (-stride) Downsample a pool of reads starting within a range of one or more bases. Default value: 1. | |
| excludeIntervals | Optional<Boolean> | –exclude-intervals | (-XLOne) This argument may be specified 0 or more times. Default value: null. | |
| f1r2MaxDepth | Optional<Integer> | –f1r2-max-depth | sites with depth higher than this value will be grouped Default value: 200. | |
| f1r2MedianMq | Optional<Integer> | –f1r2-median-mq | skip sites with median mapping quality below this value Default value: 50. | |
| f1r2MinBq | Optional<Integer> | –f1r2-min-bq | exclude bases below this quality from pileup Default value: 20. | |
| f1r2TarGz_outputFilename | Optional<Filename> | –f1r2-tar-gz | If specified, collect F1R2 counts and output files into this tar.gz file Default value: null. | |
| founderId | Optional<String> | -founder-id | (–founder-id) Samples representing the population founders This argument may be specified 0 or more times. Default value: null. | |
| gatkConfigFile | Optional<String> | –gatk-config-file | A configuration file to use with the GATK. Default value: null. | |
| gcsRetries | Optional<Integer> | -gcs-retries | (–gcs-max-retries) If the GCS bucket channel errors out, how many times it will attempt to re-initiate the connection Default value: 20. | |
| gcsProjectForRequesterPays | Optional<String> | –gcs-project-for-requester-pays | Project to bill when accessing requester pays buckets. If unset, these buckets cannot be accessed. Default value: . | |
| genotypeGermlineSites | Optional<Boolean> | –genotype-germline-sites | (EXPERIMENTAL) Call all apparent germline site even though they will ultimately be filtered. Default value: false. Possible values: {true, false} | |
| genotypePonSites | Optional<Boolean> | –genotype-pon-sites | Call sites in the PoN even though they will ultimately be filtered. Default value: false. Possible values: {true, false} | |
| germlineResource | Optional<Gzipped<VCF>> | –germline-resource | Population vcf of germline sequencing containing allele fractions. Default value: null. | |
| graph | Optional<String> | -graph | (–graph-output) Write debug assembly graph information to this file Default value: null. | |
| help | Optional<Boolean> | -h | (–help) display the help message Default value: false. Possible values: {true, false} | |
| ignoreItrArtifacts | Optional<String> | –ignore-itr-artifactsTurn | inverted tandem repeats. Default value: false. Possible values: {true, false} | |
| initialTumorLod | Optional<String> | –initial-tumor-lod | (-init-lod) Log 10 odds threshold to consider pileup active. Default value: 2.0. | |
| intervalExclusionPadding | Optional<String> | –interval-exclusion-padding | (-ixp) Amount of padding (in bp) to add to each interval you are excluding. Default value: 0. | |
| imr | Optional<String> | –interval-merging-rule | (–interval-merging-rule) Interval merging rule for abutting intervals Default value: ALL. Possible values: {ALL, OVERLAPPING_ONLY} | |
| ip | Optional<String> | -ipAmount | (–interval-padding) Default value: 0. | |
| isr | Optional<String> | –interval-set-rule | (–interval-set-rule) Set merging approach to use for combining interval inputs Default value: UNION. Possible values: {UNION, INTERSECTION} | |
| intervals | Optional<bed> | –intervals | (-L) One or more genomic intervals over which to operate This argument may be specified 0 or more times. Default value: null. | |
| le | Optional<Boolean> | -LE | (–lenient) Lenient processing of VCF files Default value: false. Possible values: {true, false} | |
| maxPopulationAf | Optional<String> | –max-population-af | (-max-af) Maximum population allele frequency in tumor-only mode. Default value: 0.01. | |
| maxReadsPerAlignmentStart | Optional<Integer> | –max-reads-per-alignment-start | Maximum number of reads to retain per alignment start position. Reads above this threshold will be downsampled. Set to 0 to disable. Default value: 50. | |
| minBaseQualityScore | Optional<String> | –min-base-quality-score | (-mbq:Byte) Minimum base quality required to consider a base for calling Default value: 10. | |
| mitochondriaMode | Optional<Boolean> | –mitochondria-mode | Mitochondria mode sets emission and initial LODs to 0. Default value: false. Possible values: {true, false} | |
| nativePairHmmThreads | Optional<Integer> | –native-pair-hmm-threads | How many threads should a native pairHMM implementation use Default value: 4. | |
| nativePairHmmUseDoublePrecision | Optional<Boolean> | –native-pair-hmm-use-double-precision | use double precision in the native pairHmm. This is slower but matches the java implementation better Default value: false. Possible values: {true, false} | |
| normalLod | Optional<Double> | –normal-lod | Log 10 odds threshold for calling normal variant non-germline. Default value: 2.2. | |
| encode | Optional<String> | -encode | This argument may be specified 0 or more times. Default value: null. | |
| panelOfNormals | Optional<Gzipped<VCF>> | –panel-of-normals | (–panel-of-normals) VCF file of sites observed in normal. Default value: null. | |
| pcrIndelQual | Optional<Integer> | –pcr-indel-qual | Phred-scaled PCR SNV qual for overlapping fragments Default value: 40. | |
| pcrSnvQual | Optional<Integer> | –pcr-snv-qual | Phred-scaled PCR SNV qual for overlapping fragments Default value: 40. | |
| pedigree | Optional<String> | –pedigree | (-ped) Pedigree file for determining the population founders. Default value: null. | |
| quiet | Optional<Boolean> | –QUIET | Whether to suppress job-summary info on System.err. Default value: false. Possible values: {true, false} | |
| readFilter | Optional<String> | –read-filter | (-RF) Read filters to be applied before analysis This argument may be specified 0 or more times. Default value: null. Possible Values: {AlignmentAgreesWithHeaderReadFilter, AllowAllReadsReadFilter, AmbiguousBaseReadFilter, CigarContainsNoNOperator, FirstOfPairReadFilter, FragmentLengthReadFilter, GoodCigarReadFilter, HasReadGroupReadFilter, IntervalOverlapReadFilter, LibraryReadFilter, MappedReadFilter, MappingQualityAvailableReadFilter, MappingQualityNotZeroReadFilter, MappingQualityReadFilter, MatchingBasesAndQualsReadFilter, MateDifferentStrandReadFilter, MateOnSameContigOrNoMappedMateReadFilter, MateUnmappedAndUnmappedReadFilter, MetricsReadFilter, NonChimericOriginalAlignmentReadFilter, NonZeroFragmentLengthReadFilter, NonZeroReferenceLengthAlignmentReadFilter, NotDuplicateReadFilter, NotOpticalDuplicateReadFilter, NotSecondaryAlignmentReadFilter, NotSupplementaryAlignmentReadFilter, OverclippedReadFilter, PairedReadFilter, PassesVendorQualityCheckReadFilter, PlatformReadFilter, PlatformUnitReadFilter, PrimaryLineReadFilter, ProperlyPairedReadFilter, ReadGroupBlackListReadFilter, ReadGroupReadFilter, ReadLengthEqualsCigarLengthReadFilter, ReadLengthReadFilter, ReadNameReadFilter, ReadStrandFilter, SampleReadFilter, SecondOfPairReadFilter, SeqIsStoredReadFilter, ValidAlignmentEndReadFilter, ValidAlignmentStartReadFilter, WellformedReadFilter} | |
| readIndex | Optional<String> | -read-index | (–read-index) Indices to use for the read inputs. If specified, an index must be provided for every read input and in the same order as the read inputs. If this argument is not specified, the path to the index for each input will be inferred automatically. This argument may be specified 0 or more times. Default value: null. | |
| readValidationStringency | Optional<String> | –read-validation-stringency | (-VS:ValidationStringency) Validation stringency for all SAM/BAM/CRAM/SRA files read by this program. The default stringency value SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded. Default value: SILENT. Possible values: {STRICT, LENIENT, SILENT} | |
| secondsBetweenProgressUpdates | Optional<Double> | -seconds-between-progress-updates | (–seconds-between-progress-updates) Output traversal statistics every time this many seconds elapse Default value: 10.0. | |
| sequenceDictionary | Optional<String> | -sequence-dictionary | (–sequence-dictionary) Use the given sequence dictionary as the master/canonical sequence dictionary. Must be a .dict file. Default value: null. | |
| sitesOnlyVcfOutput | Optional<Boolean> | –sites-only-vcf-output | If true, don’t emit genotype fields when writing vcf file output. Default value: false. Possible values: {true, false} | |
| tmpDir | Optional<String> | –tmp-dir | Temp directory to use. Default value: null. | |
| tumorLodToEmit | Optional<String> | –tumor-lod-to-emit | (-emit-lod) Log 10 odds threshold to emit variant to VCF. Default value: 3.0. | |
| tumor | Optional<String> | -tumor | (–tumor-sample) BAM sample name of tumor. May be URL-encoded as output by GetSampleName with -encode argument. Default value: null. | |
| jdkDeflater | Optional<Boolean> | -jdk-deflater | (–use-jdk-deflater) Whether to use the JdkDeflater (as opposed to IntelDeflater) Default value: false. Possible values: {true, false} | |
| jdkInflater | Optional<Boolean> | -jdk-inflater | (–use-jdk-inflater) Whether to use the JdkInflater (as opposed to IntelInflater) Default value: false. Possible values: {true, false} | |
| verbosity | Optional<String> | -verbosity | (–verbosity) Control verbosity of logging. Default value: INFO. Possible values: {ERROR, WARNING, INFO, DEBUG} | |
| version | Optional<Boolean> | –version | display the version number for this tool Default value: false. Possible values: {true, false} | |
| activeProbabilityThreshold | Optional<Double> | –active-probability-threshold | Minimum probability for a locus to be considered active. Default value: 0.002. | |
| adaptivePruningInitialErrorRate | Optional<Double> | –adaptive-pruning-initial-error-rate | Initial base error rate estimate for adaptive pruning Default value: 0.001. | |
| allowNonUniqueKmersInRef | Optional<Boolean> | –allow-non-unique-kmers-in-ref | Allow graphs that have non-unique kmers in the reference Default value: false. Possible values: {true, false} | |
| assemblyRegionPadding | Optional<Integer> | –assembly-region-padding | Number of additional bases of context to include around each assembly region Default value: 100. | |
| bamWriterType | Optional<String> | –bam-writer-type | Which haplotypes should be written to the BAM Default value: CALLED_HAPLOTYPES. Possible values: {ALL_POSSIBLE_HAPLOTYPES, CALLED_HAPLOTYPES} | |
| debugAssembly | Optional<String> | –debug-assembly | (-debug) Print out verbose debug information about each assembly region Default value: false. Possible values: {true, false} | |
| disableAdaptivePruning | Optional<Boolean> | –disable-adaptive-pruning | Disable the adaptive algorithm for pruning paths in the graph Default value: false. Possible values: {true, false} | |
| disableToolDefaultAnnotations | Optional<Boolean> | -disable-tool-default-annotations | (–disable-tool-default-annotations) Disable all tool default annotations Default value: false. Possible values: {true, false} | |
| disableToolDefaultReadFilters | Optional<Boolean> | -disable-tool-default-read-filters | (–disable-tool-default-read-filters) Disable all tool default read filters (WARNING: many tools will not function correctly without their default read filters on) Default value: false. Possible values: {true, false} | |
| dontIncreaseKmerSizesForCycles | Optional<Boolean> | –dont-increase-kmer-sizes-for-cycles | Disable iterating over kmer sizes when graph cycles are detected Default value: false. Possible values: {true, false} | |
| dontTrimActiveRegions | Optional<Boolean> | –dont-trim-active-regions | If specified, we will not trim down the active region from the full region (active + extension) to just the active interval for genotyping Default value: false. Possible values: {true, false} | |
| dontUseSoftClippedBases | Optional<Boolean> | –dont-use-soft-clipped-bases | Do not analyze soft clipped bases in the reads Default value: false. Possible values: {true, false} | |
| erc | Optional<String> | -ERC | (–emit-ref-confidence) (BETA feature) Mode for emitting reference confidence scores Default value: NONE. Possible values: {NONE, BP_RESOLUTION, GVCF} | |
| enableAllAnnotations | Optional<Boolean> | –enable-all-annotations | Use all possible annotations (not for the faint of heart) Default value: false. Possible values: {true, false} | |
| forceActive | Optional<Boolean> | –force-active | If provided, all regions will be marked as active Default value: false. Possible values: {true, false} | |
| genotypeFilteredAlleles | Optional<Boolean> | –genotype-filtered-alleles | Whether to force genotype even filtered alleles Default value: false. Possible values: {true, false} | |
| gvcfLodBand | Optional<String> | –gvcf-lod-band | (-LODB) Exclusive upper bounds for reference confidence LOD bands (must be specified in increasing order) This argument may be specified 0 or more times. Default value: [-2.5, -2.0, -1.5, | |
| kmerSize | Optional<Integer> | –kmer-size | Kmer size to use in the read threading assembler This argument may be specified 0 or more times. Default value: [10, 25]. | |
| maxAssemblyRegionSize | Optional<Integer> | –max-assembly-region-size | Maximum size of an assembly region Default value: 300. | |
| mnpDist | Optional<Integer> | -mnp-dist | (–max-mnp-distance) Two or more phased substitutions separated by this distance or less are merged into MNPs. Default value: 1. | |
| maxNumHaplotypesInPopulation | Optional<Integer> | –max-num-haplotypes-in-population | Maximum number of haplotypes to consider for your population Default value: 128. | |
| maxProbPropagationDistance | Optional<Integer> | –max-prob-propagation-distance | Upper limit on how many bases away probability mass can be moved around when calculating the boundaries between active and inactive assembly regions Default value: 50. | |
| maxSuspiciousReadsPerAlignmentStart | Optional<Integer> | –max-suspicious-reads-per-alignment-start | Maximum number of suspicious reads (mediocre mapping quality or too many substitutions) allowed in a downsampling stride. Set to 0 to disable. Default value: 0. | |
| maxUnprunedVariants | Optional<Integer> | –max-unpruned-variants | Maximum number of variants in graph the adaptive pruner will allow Default value: 100. | |
| minAssemblyRegionSize | Optional<Integer> | –min-assembly-region-size | Minimum size of an assembly region Default value: 50. | |
| minDanglingBranchLength | Optional<Integer> | –min-dangling-branch-length | Minimum length of a dangling branch to attempt recovery Default value: 4. | |
| minPruning | Optional<Integer> | –min-pruning | Minimum support to not prune paths in the graph Default value: 2. | |
| minimumAlleleFraction | Optional<Float> | –minimum-allele-fraction | (-min-AF) Lower bound of variant allele fractions to consider when calculating variant LOD Default value: 0.0. | |
| numPruningSamples | Optional<Integer> | –num-pruning-samples | Default value: 1. | |
| pairHmmGapContinuationPenalty | Optional<Integer> | –pair-hmm-gap-continuation-penalty | Flat gap continuation penalty for use in the Pair HMM Default value: 10. | |
| pairhmm | Optional<String> | -pairHMM | (–pair-hmm-implementation) The PairHMM implementation to use for genotype likelihood calculations Default value: FASTEST_AVAILABLE. Possible values: {EXACT, ORIGINAL, LOGLESS_CACHING, AVX_LOGLESS_CACHING, AVX_LOGLESS_CACHING_OMP, EXPERIMENTAL_FPGA_LOGLESS_CACHING, FASTEST_AVAILABLE} | |
| pcrIndelModel | Optional<String> | –pcr-indel-model | The PCR indel model to use Default value: CONSERVATIVE. Possible values: {NONE, HOSTILE, AGGRESSIVE, CONSERVATIVE} | |
| phredScaledGlobalReadMismappingRate | Optional<Integer> | –phred-scaled-global-read-mismapping-rate | The global assumed mismapping rate for reads Default value: 45. | |
| pruningLodThreshold | Optional<Float> | –pruning-lod-thresholdLn | Default value: 2.302585092994046. | |
| recoverAllDanglingBranches | Optional<Boolean> | –recover-all-dangling-branches | Recover all dangling branches Default value: false. Possible values: {true, false} | |
| showhidden | Optional<Boolean> | -showHidden | (–showHidden) display hidden arguments Default value: false. Possible values: {true, false} | |
| smithWaterman | Optional<String> | –smith-waterman | Which Smith-Waterman implementation to use, generally FASTEST_AVAILABLE is the right choice Default value: JAVA. Possible values: {FASTEST_AVAILABLE, AVX_ENABLED, JAVA} | |
| ambigFilterBases | Optional<Integer> | –ambig-filter-bases | Threshold number of ambiguous bases. If null, uses threshold fraction; otherwise, overrides threshold fraction. Default value: null. Cannot be used in conjuction with argument(s) maxAmbiguousBaseFraction | |
| ambigFilterFrac | Optional<Double> | –ambig-filter-frac | Threshold fraction of ambiguous bases Default value: 0.05. Cannot be used in conjuction with argument(s) maxAmbiguousBases | |
| maxFragmentLength | Optional<Integer> | –max-fragment-length | Default value: 1000000. | |
| minFragmentLength | Optional<Integer> | –min-fragment-length | Default value: 0. | |
| keepIntervals | Optional<String> | –keep-intervals | One or more genomic intervals to keep This argument must be specified at least once. Required. | |
| library | Optional<String> | -library | (–library) Name of the library to keep This argument must be specified at least once. Required. | |
| maximumMappingQuality | Optional<Integer> | –maximum-mapping-quality | Maximum mapping quality to keep (inclusive) Default value: null. | |
| minimumMappingQuality | Optional<Integer> | –minimum-mapping-quality | Minimum mapping quality to keep (inclusive) Default value: 20. | |
| dontRequireSoftClipsBothEnds | Optional<Boolean> | –dont-require-soft-clips-both-ends | Allow a read to be filtered out based on having only 1 soft-clipped block. By default, both ends must have a soft-clipped block, setting this flag requires only 1 soft-clipped block Default value: false. Possible values: {true, false} | |
| filterTooShort | Optional<Integer> | –filter-too-short | Minimum number of aligned bases Default value: 30. | |
| platformFilterName | Optional<String> | –platform-filter-name | This argument must be specified at least once. Required. | |
| blackListedLanes | Optional<String> | –black-listed-lanes | Platform unit (PU) to filter out This argument must be specified at least once. Required. | |
| readGroupBlackList | Optional<String> | –read-group-black-listThe | This argument must be specified at least once. Required. | |
| keepReadGroup | Optional<String> | –keep-read-group | The name of the read group to keep Required. | |
| maxReadLength | Optional<Integer> | –max-read-length | Keep only reads with length at most equal to the specified value Default value: 2147483647. | |
| minReadLength | Optional<Integer> | –min-read-length | Keep only reads with length at least equal to the specified value Default value: 30. | |
| readName | Optional<String> | –read-name | Keep only reads with this read name Required. | |
| keepReverseStrandOnly | Optional<Boolean> | –keep-reverse-strand-only | Keep only reads on the reverse strand Required. Possible values: {true, false} | |
| sample | Optional<String> | -sample | (–sample) The name of the sample(s) to keep, filtering out all others This argument must be specified at least once. Required. |
Workflow Description Language¶
version development
task Gatk4Mutect2 {
input {
Int? runtime_cpu
Int? runtime_memory
Int? runtime_seconds
Int? runtime_disks
Array[String]? javaOptions
Int? compression_level
Array[File] tumorBams
Array[File] tumorBams_bai
Array[File]? normalBams
Array[File]? normalBams_bai
String? normalSample
String? outputPrefix
String? outputFilename
File reference
File reference_fai
File reference_amb
File reference_ann
File reference_bwt
File reference_pac
File reference_sa
File reference_dict
String? outputBamName
String? activityProfileOut
Boolean? addOutputSamProgramRecord
Boolean? addOutputVcfCommandLine
String? afOfAllelesNotInResource
String? alleles
String? annotation
String? annotationGroup
String? annotationsToExclude
File? arguments_file
String? assemblyRegionOut
Int? baseQualityScoreThreshold
Int? callableDepth
Int? cloudIndexPrefetchBuffer
Int? cloudPrefetchBuffer
Boolean? createOutputBamIndex
Boolean? createOutputBamMd5
Boolean? createOutputVariantIndex
Boolean? createOutputVariantMd5
Boolean? disableBamIndexCaching
Boolean? disableReadFilter
Boolean? disableSequenceDictionaryValidation
Int? downsamplingStride
Boolean? excludeIntervals
Int? f1r2MaxDepth
Int? f1r2MedianMq
Int? f1r2MinBq
String? f1r2TarGz_outputFilename
String? founderId
String? gatkConfigFile
Int? gcsRetries
String? gcsProjectForRequesterPays
Boolean? genotypeGermlineSites
Boolean? genotypePonSites
File? germlineResource
File? germlineResource_tbi
String? graph
Boolean? help
String? ignoreItrArtifacts
String? initialTumorLod
String? intervalExclusionPadding
String? imr
String? ip
String? isr
File? intervals
Boolean? le
String? maxPopulationAf
Int? maxReadsPerAlignmentStart
String? minBaseQualityScore
Boolean? mitochondriaMode
Int? nativePairHmmThreads
Boolean? nativePairHmmUseDoublePrecision
Float? normalLod
String? encode
File? panelOfNormals
File? panelOfNormals_tbi
Int? pcrIndelQual
Int? pcrSnvQual
String? pedigree
Boolean? quiet
String? readFilter
String? readIndex
String? readValidationStringency
Float? secondsBetweenProgressUpdates
String? sequenceDictionary
Boolean? sitesOnlyVcfOutput
String? tmpDir
String? tumorLodToEmit
String? tumor
Boolean? jdkDeflater
Boolean? jdkInflater
String? verbosity
Boolean? version
Float? activeProbabilityThreshold
Float? adaptivePruningInitialErrorRate
Boolean? allowNonUniqueKmersInRef
Int? assemblyRegionPadding
String? bamWriterType
String? debugAssembly
Boolean? disableAdaptivePruning
Boolean? disableToolDefaultAnnotations
Boolean? disableToolDefaultReadFilters
Boolean? dontIncreaseKmerSizesForCycles
Boolean? dontTrimActiveRegions
Boolean? dontUseSoftClippedBases
String? erc
Boolean? enableAllAnnotations
Boolean? forceActive
Boolean? genotypeFilteredAlleles
String? gvcfLodBand
Int? kmerSize
Int? maxAssemblyRegionSize
Int? mnpDist
Int? maxNumHaplotypesInPopulation
Int? maxProbPropagationDistance
Int? maxSuspiciousReadsPerAlignmentStart
Int? maxUnprunedVariants
Int? minAssemblyRegionSize
Int? minDanglingBranchLength
Int? minPruning
Float? minimumAlleleFraction
Int? numPruningSamples
Int? pairHmmGapContinuationPenalty
String? pairhmm
String? pcrIndelModel
Int? phredScaledGlobalReadMismappingRate
Float? pruningLodThreshold
Boolean? recoverAllDanglingBranches
Boolean? showhidden
String? smithWaterman
Int? ambigFilterBases
Float? ambigFilterFrac
Int? maxFragmentLength
Int? minFragmentLength
String? keepIntervals
String? library
Int? maximumMappingQuality
Int? minimumMappingQuality
Boolean? dontRequireSoftClipsBothEnds
Int? filterTooShort
String? platformFilterName
String? blackListedLanes
String? readGroupBlackList
String? keepReadGroup
Int? maxReadLength
Int? minReadLength
String? readName
Boolean? keepReverseStrandOnly
String? sample
}
command <<<
set -e
gatk Mutect2 \
--java-options '-Xmx~{((select_first([runtime_memory, 16, 4]) * 3) / 4)}G ~{if (defined(compression_level)) then ("-Dsamjdk.compress_level=" + compression_level) else ""} ~{sep(" ", select_first([javaOptions, []]))}' \
~{if length(tumorBams) > 0 then "-I '" + sep("' -I '", tumorBams) + "'" else ""} \
~{if (defined(normalBams) && length(select_first([normalBams])) > 0) then "-I '" + sep("' -I '", select_first([normalBams])) + "'" else ""} \
~{if defined(normalSample) then ("--normal-sample '" + normalSample + "'") else ""} \
--reference '~{reference}' \
~{if defined(outputBamName) then ("-bamout '" + outputBamName + "'") else ""} \
~{if defined(activityProfileOut) then ("--activity-profile-out '" + activityProfileOut + "'") else ""} \
~{if (defined(addOutputSamProgramRecord) && select_first([addOutputSamProgramRecord])) then "-add-output-sam-program-record" else ""} \
~{if (defined(addOutputVcfCommandLine) && select_first([addOutputVcfCommandLine])) then "-add-output-vcf-command-line" else ""} \
~{if defined(afOfAllelesNotInResource) then ("--af-of-alleles-not-in-resource '" + afOfAllelesNotInResource + "'") else ""} \
~{if defined(alleles) then ("--alleles '" + alleles + "'") else ""} \
~{if defined(annotation) then ("--annotation '" + annotation + "'") else ""} \
~{if defined(annotationGroup) then ("--annotation-group '" + annotationGroup + "'") else ""} \
~{if defined(annotationsToExclude) then ("--annotations-to-exclude '" + annotationsToExclude + "'") else ""} \
~{if defined(arguments_file) then ("--arguments_file '" + arguments_file + "'") else ""} \
~{if defined(assemblyRegionOut) then ("--assembly-region-out '" + assemblyRegionOut + "'") else ""} \
~{if defined(baseQualityScoreThreshold) then ("--base-quality-score-threshold " + baseQualityScoreThreshold) else ''} \
~{if defined(callableDepth) then ("--callable-depth " + callableDepth) else ''} \
~{if defined(cloudIndexPrefetchBuffer) then ("--cloud-index-prefetch-buffer " + cloudIndexPrefetchBuffer) else ''} \
~{if defined(cloudPrefetchBuffer) then ("--cloud-prefetch-buffer " + cloudPrefetchBuffer) else ''} \
~{if (defined(createOutputBamIndex) && select_first([createOutputBamIndex])) then "--create-output-bam-index" else ""} \
~{if (defined(createOutputBamMd5) && select_first([createOutputBamMd5])) then "--create-output-bam-md5" else ""} \
~{if (defined(createOutputVariantIndex) && select_first([createOutputVariantIndex])) then "--create-output-variant-index" else ""} \
~{if (defined(createOutputVariantMd5) && select_first([createOutputVariantMd5])) then "--create-output-variant-md5" else ""} \
~{if (defined(disableBamIndexCaching) && select_first([disableBamIndexCaching])) then "--disable-bam-index-caching" else ""} \
~{if (defined(disableReadFilter) && select_first([disableReadFilter])) then "--disable-read-filter" else ""} \
~{if (defined(disableSequenceDictionaryValidation) && select_first([disableSequenceDictionaryValidation])) then "-disable-sequence-dictionary-validation" else ""} \
~{if defined(downsamplingStride) then ("--downsampling-stride " + downsamplingStride) else ''} \
~{if (defined(excludeIntervals) && select_first([excludeIntervals])) then "--exclude-intervals" else ""} \
~{if defined(f1r2MaxDepth) then ("--f1r2-max-depth " + f1r2MaxDepth) else ''} \
~{if defined(f1r2MedianMq) then ("--f1r2-median-mq " + f1r2MedianMq) else ''} \
~{if defined(f1r2MinBq) then ("--f1r2-min-bq " + f1r2MinBq) else ''} \
--f1r2-tar-gz '~{select_first([f1r2TarGz_outputFilename, "generated.tar.gz"])}' \
~{if defined(founderId) then ("-founder-id '" + founderId + "'") else ""} \
~{if defined(gatkConfigFile) then ("--gatk-config-file '" + gatkConfigFile + "'") else ""} \
~{if defined(gcsRetries) then ("-gcs-retries " + gcsRetries) else ''} \
~{if defined(gcsProjectForRequesterPays) then ("--gcs-project-for-requester-pays '" + gcsProjectForRequesterPays + "'") else ""} \
~{if (defined(genotypeGermlineSites) && select_first([genotypeGermlineSites])) then "--genotype-germline-sites" else ""} \
~{if (defined(genotypePonSites) && select_first([genotypePonSites])) then "--genotype-pon-sites" else ""} \
~{if defined(germlineResource) then ("--germline-resource '" + germlineResource + "'") else ""} \
~{if defined(graph) then ("-graph '" + graph + "'") else ""} \
~{if (defined(help) && select_first([help])) then "-h" else ""} \
~{if defined(ignoreItrArtifacts) then ("--ignore-itr-artifactsTurn '" + ignoreItrArtifacts + "'") else ""} \
~{if defined(initialTumorLod) then ("--initial-tumor-lod '" + initialTumorLod + "'") else ""} \
~{if defined(intervalExclusionPadding) then ("--interval-exclusion-padding '" + intervalExclusionPadding + "'") else ""} \
~{if defined(imr) then ("--interval-merging-rule '" + imr + "'") else ""} \
~{if defined(ip) then ("-ipAmount '" + ip + "'") else ""} \
~{if defined(isr) then ("--interval-set-rule '" + isr + "'") else ""} \
~{if defined(intervals) then ("--intervals '" + intervals + "'") else ""} \
~{if (defined(le) && select_first([le])) then "-LE" else ""} \
~{if defined(maxPopulationAf) then ("--max-population-af '" + maxPopulationAf + "'") else ""} \
~{if defined(maxReadsPerAlignmentStart) then ("--max-reads-per-alignment-start " + maxReadsPerAlignmentStart) else ''} \
~{if defined(minBaseQualityScore) then ("--min-base-quality-score '" + minBaseQualityScore + "'") else ""} \
~{if (defined(mitochondriaMode) && select_first([mitochondriaMode])) then "--mitochondria-mode" else ""} \
~{if defined(select_first([nativePairHmmThreads, select_first([runtime_cpu, 1])])) then ("--native-pair-hmm-threads " + select_first([nativePairHmmThreads, select_first([runtime_cpu, 1])])) else ''} \
~{if (defined(nativePairHmmUseDoublePrecision) && select_first([nativePairHmmUseDoublePrecision])) then "--native-pair-hmm-use-double-precision" else ""} \
~{if defined(normalLod) then ("--normal-lod " + normalLod) else ''} \
~{if defined(encode) then ("-encode '" + encode + "'") else ""} \
~{if defined(panelOfNormals) then ("--panel-of-normals '" + panelOfNormals + "'") else ""} \
~{if defined(pcrIndelQual) then ("--pcr-indel-qual " + pcrIndelQual) else ''} \
~{if defined(pcrSnvQual) then ("--pcr-snv-qual " + pcrSnvQual) else ''} \
~{if defined(pedigree) then ("--pedigree '" + pedigree + "'") else ""} \
~{if (defined(quiet) && select_first([quiet])) then "--QUIET" else ""} \
~{if defined(readFilter) then ("--read-filter '" + readFilter + "'") else ""} \
~{if defined(readIndex) then ("-read-index '" + readIndex + "'") else ""} \
~{if defined(readValidationStringency) then ("--read-validation-stringency '" + readValidationStringency + "'") else ""} \
~{if defined(secondsBetweenProgressUpdates) then ("-seconds-between-progress-updates " + secondsBetweenProgressUpdates) else ''} \
~{if defined(sequenceDictionary) then ("-sequence-dictionary '" + sequenceDictionary + "'") else ""} \
~{if (defined(sitesOnlyVcfOutput) && select_first([sitesOnlyVcfOutput])) then "--sites-only-vcf-output" else ""} \
~{if defined(tmpDir) then ("--tmp-dir '" + tmpDir + "'") else ""} \
~{if defined(tumorLodToEmit) then ("--tumor-lod-to-emit '" + tumorLodToEmit + "'") else ""} \
~{if defined(tumor) then ("-tumor '" + tumor + "'") else ""} \
~{if (defined(jdkDeflater) && select_first([jdkDeflater])) then "-jdk-deflater" else ""} \
~{if (defined(jdkInflater) && select_first([jdkInflater])) then "-jdk-inflater" else ""} \
~{if defined(verbosity) then ("-verbosity '" + verbosity + "'") else ""} \
~{if (defined(version) && select_first([version])) then "--version" else ""} \
~{if defined(activeProbabilityThreshold) then ("--active-probability-threshold " + activeProbabilityThreshold) else ''} \
~{if defined(adaptivePruningInitialErrorRate) then ("--adaptive-pruning-initial-error-rate " + adaptivePruningInitialErrorRate) else ''} \
~{if (defined(allowNonUniqueKmersInRef) && select_first([allowNonUniqueKmersInRef])) then "--allow-non-unique-kmers-in-ref" else ""} \
~{if defined(assemblyRegionPadding) then ("--assembly-region-padding " + assemblyRegionPadding) else ''} \
~{if defined(bamWriterType) then ("--bam-writer-type '" + bamWriterType + "'") else ""} \
~{if defined(debugAssembly) then ("--debug-assembly '" + debugAssembly + "'") else ""} \
~{if (defined(disableAdaptivePruning) && select_first([disableAdaptivePruning])) then "--disable-adaptive-pruning" else ""} \
~{if (defined(disableToolDefaultAnnotations) && select_first([disableToolDefaultAnnotations])) then "-disable-tool-default-annotations" else ""} \
~{if (defined(disableToolDefaultReadFilters) && select_first([disableToolDefaultReadFilters])) then "-disable-tool-default-read-filters" else ""} \
~{if (defined(dontIncreaseKmerSizesForCycles) && select_first([dontIncreaseKmerSizesForCycles])) then "--dont-increase-kmer-sizes-for-cycles" else ""} \
~{if (defined(dontTrimActiveRegions) && select_first([dontTrimActiveRegions])) then "--dont-trim-active-regions" else ""} \
~{if (defined(dontUseSoftClippedBases) && select_first([dontUseSoftClippedBases])) then "--dont-use-soft-clipped-bases" else ""} \
~{if defined(erc) then ("-ERC '" + erc + "'") else ""} \
~{if (defined(enableAllAnnotations) && select_first([enableAllAnnotations])) then "--enable-all-annotations" else ""} \
~{if (defined(forceActive) && select_first([forceActive])) then "--force-active" else ""} \
~{if (defined(genotypeFilteredAlleles) && select_first([genotypeFilteredAlleles])) then "--genotype-filtered-alleles" else ""} \
~{if defined(gvcfLodBand) then ("--gvcf-lod-band '" + gvcfLodBand + "'") else ""} \
~{if defined(kmerSize) then ("--kmer-size " + kmerSize) else ''} \
~{if defined(maxAssemblyRegionSize) then ("--max-assembly-region-size " + maxAssemblyRegionSize) else ''} \
~{if defined(mnpDist) then ("-mnp-dist " + mnpDist) else ''} \
~{if defined(maxNumHaplotypesInPopulation) then ("--max-num-haplotypes-in-population " + maxNumHaplotypesInPopulation) else ''} \
~{if defined(maxProbPropagationDistance) then ("--max-prob-propagation-distance " + maxProbPropagationDistance) else ''} \
~{if defined(maxSuspiciousReadsPerAlignmentStart) then ("--max-suspicious-reads-per-alignment-start " + maxSuspiciousReadsPerAlignmentStart) else ''} \
~{if defined(maxUnprunedVariants) then ("--max-unpruned-variants " + maxUnprunedVariants) else ''} \
~{if defined(minAssemblyRegionSize) then ("--min-assembly-region-size " + minAssemblyRegionSize) else ''} \
~{if defined(minDanglingBranchLength) then ("--min-dangling-branch-length " + minDanglingBranchLength) else ''} \
~{if defined(minPruning) then ("--min-pruning " + minPruning) else ''} \
~{if defined(minimumAlleleFraction) then ("--minimum-allele-fraction " + minimumAlleleFraction) else ''} \
~{if defined(numPruningSamples) then ("--num-pruning-samples " + numPruningSamples) else ''} \
~{if defined(pairHmmGapContinuationPenalty) then ("--pair-hmm-gap-continuation-penalty " + pairHmmGapContinuationPenalty) else ''} \
~{if defined(pairhmm) then ("-pairHMM '" + pairhmm + "'") else ""} \
~{if defined(pcrIndelModel) then ("--pcr-indel-model '" + pcrIndelModel + "'") else ""} \
~{if defined(phredScaledGlobalReadMismappingRate) then ("--phred-scaled-global-read-mismapping-rate " + phredScaledGlobalReadMismappingRate) else ''} \
~{if defined(pruningLodThreshold) then ("--pruning-lod-thresholdLn " + pruningLodThreshold) else ''} \
~{if (defined(recoverAllDanglingBranches) && select_first([recoverAllDanglingBranches])) then "--recover-all-dangling-branches" else ""} \
~{if (defined(showhidden) && select_first([showhidden])) then "-showHidden" else ""} \
~{if defined(smithWaterman) then ("--smith-waterman '" + smithWaterman + "'") else ""} \
~{if defined(ambigFilterBases) then ("--ambig-filter-bases " + ambigFilterBases) else ''} \
~{if defined(ambigFilterFrac) then ("--ambig-filter-frac " + ambigFilterFrac) else ''} \
~{if defined(maxFragmentLength) then ("--max-fragment-length " + maxFragmentLength) else ''} \
~{if defined(minFragmentLength) then ("--min-fragment-length " + minFragmentLength) else ''} \
~{if defined(keepIntervals) then ("--keep-intervals '" + keepIntervals + "'") else ""} \
~{if defined(library) then ("-library '" + library + "'") else ""} \
~{if defined(maximumMappingQuality) then ("--maximum-mapping-quality " + maximumMappingQuality) else ''} \
~{if defined(minimumMappingQuality) then ("--minimum-mapping-quality " + minimumMappingQuality) else ''} \
~{if (defined(dontRequireSoftClipsBothEnds) && select_first([dontRequireSoftClipsBothEnds])) then "--dont-require-soft-clips-both-ends" else ""} \
~{if defined(filterTooShort) then ("--filter-too-short " + filterTooShort) else ''} \
~{if defined(platformFilterName) then ("--platform-filter-name '" + platformFilterName + "'") else ""} \
~{if defined(blackListedLanes) then ("--black-listed-lanes '" + blackListedLanes + "'") else ""} \
~{if defined(readGroupBlackList) then ("--read-group-black-listThe '" + readGroupBlackList + "'") else ""} \
~{if defined(keepReadGroup) then ("--keep-read-group '" + keepReadGroup + "'") else ""} \
~{if defined(maxReadLength) then ("--max-read-length " + maxReadLength) else ''} \
~{if defined(minReadLength) then ("--min-read-length " + minReadLength) else ''} \
~{if defined(readName) then ("--read-name '" + readName + "'") else ""} \
~{if (defined(keepReverseStrandOnly) && select_first([keepReverseStrandOnly])) then "--keep-reverse-strand-only" else ""} \
~{if defined(sample) then ("-sample '" + sample + "'") else ""} \
-O '~{select_first([outputFilename, "~{select_first([outputPrefix, "generated"])}.vcf.gz"])}'
if [ -f $(echo '~{outputBamName}' | sed 's/\.[^.]*$//').bai ]; then ln -f $(echo '~{outputBamName}' | sed 's/\.[^.]*$//').bai $(echo '~{outputBamName}' ).bai; fi
>>>
runtime {
cpu: select_first([runtime_cpu, 4, 1])
disks: "local-disk ~{select_first([runtime_disks, 20])} SSD"
docker: "broadinstitute/gatk:4.1.8.1"
duration: select_first([runtime_seconds, 86400])
memory: "~{select_first([runtime_memory, 16, 4])}G"
preemptible: 2
}
output {
File out = select_first([outputFilename, "~{select_first([outputPrefix, "generated"])}.vcf.gz"])
File out_tbi = select_first([outputFilename, "~{select_first([outputPrefix, "generated"])}.vcf.gz"]) + ".tbi"
File stats = (select_first([outputFilename, "~{select_first([outputPrefix, "generated"])}.vcf.gz"]) + ".stats")
File f1f2r_out = select_first([f1r2TarGz_outputFilename, "generated.tar.gz"])
File? bam = outputBamName
File? bam_bai = if defined(outputBamName) then (outputBamName + ".bai") else None
}
}
Common Workflow Language¶
#!/usr/bin/env cwl-runner
class: CommandLineTool
cwlVersion: v1.2
label: GatkMutect2
doc: |
USAGE: Mutect2 [arguments]
Call somatic SNVs and indels via local assembly of haplotypes
Version:4.1.2.0
requirements:
- class: ShellCommandRequirement
- class: InlineJavascriptRequirement
- class: DockerRequirement
dockerPull: broadinstitute/gatk:4.1.8.1
inputs:
- id: javaOptions
label: javaOptions
type:
- type: array
items: string
- 'null'
- id: compression_level
label: compression_level
doc: |-
Compression level for all compressed files created (e.g. BAM and VCF). Default value: 2.
type:
- int
- 'null'
- id: tumorBams
label: tumorBams
doc: |-
(--input) BAM/SAM/CRAM file containing reads This argument must be specified at least once. Required.
type:
type: array
inputBinding:
prefix: -I
items: File
inputBinding: {}
- id: normalBams
label: normalBams
doc: |-
(--input) Extra BAM/SAM/CRAM file containing reads This argument must be specified at least once. Required.
type:
- type: array
inputBinding:
prefix: -I
items: File
- 'null'
inputBinding: {}
- id: normalSample
label: normalSample
doc: (--normal-sample, if) May be URL-encoded as output by GetSampleName with
type:
- string
- 'null'
inputBinding:
prefix: --normal-sample
- id: outputPrefix
label: outputPrefix
doc: |-
Used as a prefix for the outputFilename if not specified, with format: {outputPrefix}.vcf.gz
type: string
default: generated
- id: outputFilename
label: outputFilename
type:
- string
- 'null'
default: generated.vcf.gz
inputBinding:
prefix: -O
position: 20
valueFrom: '$(inputs.outputPrefix ? inputs.outputPrefix : "generated").vcf.gz'
- id: reference
label: reference
doc: (-R) Reference sequence file Required.
type: File
secondaryFiles:
- pattern: .fai
- pattern: .amb
- pattern: .ann
- pattern: .bwt
- pattern: .pac
- pattern: .sa
- pattern: ^.dict
inputBinding:
prefix: --reference
- id: outputBamName
label: outputBamName
doc: File to which assembled haplotypes should be written
type:
- string
- 'null'
inputBinding:
prefix: -bamout
- id: activityProfileOut
label: activityProfileOut
doc: 'Default value: null.'
type:
- string
- 'null'
inputBinding:
prefix: --activity-profile-out
- id: addOutputSamProgramRecord
label: addOutputSamProgramRecord
doc: |-
(--add-output-sam-program-record) If true, adds a PG tag to created SAM/BAM/CRAM files. Default value: true. Possible values: {true, false}
type:
- boolean
- 'null'
inputBinding:
prefix: -add-output-sam-program-record
- id: addOutputVcfCommandLine
label: addOutputVcfCommandLine
doc: |-
(--add-output-vcf-command-line) If true, adds a command line header line to created VCF files. Default value: true. Possible values: {true, false}
type:
- boolean
- 'null'
inputBinding:
prefix: -add-output-vcf-command-line
- id: afOfAllelesNotInResource
label: afOfAllelesNotInResource
doc: |-
(-default-af) Population allele fraction assigned to alleles not found in germline resource. Please see docs/mutect/mutect2.pdf fora derivation of the default value. Default value: -1.0.
type:
- string
- 'null'
inputBinding:
prefix: --af-of-alleles-not-in-resource
- id: alleles
label: alleles
doc: |-
The set of alleles for which to force genotyping regardless of evidence Default value: null.
type:
- string
- 'null'
inputBinding:
prefix: --alleles
- id: annotation
label: annotation
doc: |-
(-A) One or more specific annotations to add to variant calls This argument may be specified 0 or more times. Default value: null. Possible Values: {AlleleFraction, AS_BaseQualityRankSumTest, AS_FisherStrand, AS_InbreedingCoeff, AS_MappingQualityRankSumTest, AS_QualByDepth, AS_ReadPosRankSumTest, AS_RMSMappingQuality, AS_StrandOddsRatio, BaseQuality, BaseQualityRankSumTest, ChromosomeCounts, ClippingRankSumTest, CountNs, Coverage, DepthPerAlleleBySample, DepthPerSampleHC, ExcessHet, FisherStrand, FragmentLength, GenotypeSummaries, InbreedingCoeff, LikelihoodRankSumTest, MappingQuality, MappingQualityRankSumTest, MappingQualityZero, OrientationBiasReadCounts, OriginalAlignment, PossibleDeNovo, QualByDepth, ReadPosition, ReadPosRankSumTest, ReferenceBases, RMSMappingQuality, SampleList, StrandBiasBySample, StrandOddsRatio, TandemRepeat, UniqueAltReadCount}
type:
- string
- 'null'
inputBinding:
prefix: --annotation
- id: annotationGroup
label: annotationGroup
doc: |-
(-G) One or more groups of annotations to apply to variant calls This argument may be specified 0 or more times. Default value: null. Possible Values: {AS_StandardAnnotation, ReducibleAnnotation, StandardAnnotation, StandardHCAnnotation, StandardMutectAnnotation}
type:
- string
- 'null'
inputBinding:
prefix: --annotation-group
- id: annotationsToExclude
label: annotationsToExclude
doc: |-
(-AX) One or more specific annotations to exclude from variant calls This argument may be specified 0 or more times. Default value: null. Possible Values: {BaseQuality, Coverage, DepthPerAlleleBySample, DepthPerSampleHC, FragmentLength, MappingQuality, OrientationBiasReadCounts, ReadPosition, StrandBiasBySample, TandemRepeat}
type:
- string
- 'null'
inputBinding:
prefix: --annotations-to-exclude
- id: arguments_file
label: arguments_file
doc: |-
read one or more arguments files and add them to the command line This argument may be specified 0 or more times. Default value: null.
type:
- File
- 'null'
inputBinding:
prefix: --arguments_file
- id: assemblyRegionOut
label: assemblyRegionOut
doc: 'Output the assembly region to this IGV formatted file Default value: null.'
type:
- string
- 'null'
inputBinding:
prefix: --assembly-region-out
- id: baseQualityScoreThreshold
label: baseQualityScoreThreshold
doc: |2-
Base qualities below this threshold will be reduced to the minimum (6) Default value: 18.
type:
- int
- 'null'
inputBinding:
prefix: --base-quality-score-threshold
- id: callableDepth
label: callableDepth
doc: |-
Minimum depth to be considered callable for Mutect stats. Does not affect genotyping. Default value: 10.
type:
- int
- 'null'
inputBinding:
prefix: --callable-depth
- id: cloudIndexPrefetchBuffer
label: cloudIndexPrefetchBuffer
doc: |-
(-CIPB) Size of the cloud-only prefetch buffer (in MB; 0 to disable). Defaults to cloudPrefetchBuffer if unset. Default value: -1.
type:
- int
- 'null'
inputBinding:
prefix: --cloud-index-prefetch-buffer
- id: cloudPrefetchBuffer
label: cloudPrefetchBuffer
doc: |-
(-CPB) Size of the cloud-only prefetch buffer (in MB; 0 to disable). Default value: 40.
type:
- int
- 'null'
inputBinding:
prefix: --cloud-prefetch-buffer
- id: createOutputBamIndex
label: createOutputBamIndex
doc: |-
(-OBI) If true, create a BAM/CRAM index when writing a coordinate-sorted BAM/CRAM file. Default value: true. Possible values: {true, false}
type:
- boolean
- 'null'
inputBinding:
prefix: --create-output-bam-index
- id: createOutputBamMd5
label: createOutputBamMd5
doc: |-
(-OBM) If true, create a MD5 digest for any BAM/SAM/CRAM file created Default value: false. Possible values: {true, false}
type:
- boolean
- 'null'
inputBinding:
prefix: --create-output-bam-md5
- id: createOutputVariantIndex
label: createOutputVariantIndex
doc: |-
(-OVI) If true, create a VCF index when writing a coordinate-sorted VCF file. Default value: true. Possible values: {true, false}
type:
- boolean
- 'null'
inputBinding:
prefix: --create-output-variant-index
- id: createOutputVariantMd5
label: createOutputVariantMd5
doc: |-
(-OVM) If true, create a a MD5 digest any VCF file created. Default value: false. Possible values: {true, false}
type:
- boolean
- 'null'
inputBinding:
prefix: --create-output-variant-md5
- id: disableBamIndexCaching
label: disableBamIndexCaching
doc: |-
(-DBIC) If true, don't cache bam indexes, this will reduce memory requirements but may harm performance if many intervals are specified. Caching is automatically disabled if there are no intervals specified. Default value: false. Possible values: {true, false}
type:
- boolean
- 'null'
inputBinding:
prefix: --disable-bam-index-caching
- id: disableReadFilter
label: disableReadFilter
doc: |-
(-DF) Read filters to be disabled before analysis This argument may be specified 0 or more times. Default value: null. Possible Values: {GoodCigarReadFilter, MappedReadFilter, MappingQualityAvailableReadFilter, MappingQualityNotZeroReadFilter, MappingQualityReadFilter, NonChimericOriginalAlignmentReadFilter, NonZeroReferenceLengthAlignmentReadFilter, NotDuplicateReadFilter, NotSecondaryAlignmentReadFilter, PassesVendorQualityCheckReadFilter, ReadLengthReadFilter, WellformedReadFilter}
type:
- boolean
- 'null'
inputBinding:
prefix: --disable-read-filter
- id: disableSequenceDictionaryValidation
label: disableSequenceDictionaryValidation
doc: |-
(--disable-sequence-dictionary-validation) If specified, do not check the sequence dictionaries from our inputs for compatibility. Use at your own risk! Default value: false. Possible values: {true, false}
type:
- boolean
- 'null'
inputBinding:
prefix: -disable-sequence-dictionary-validation
- id: downsamplingStride
label: downsamplingStride
doc: |-
(-stride) Downsample a pool of reads starting within a range of one or more bases. Default value: 1.
type:
- int
- 'null'
inputBinding:
prefix: --downsampling-stride
- id: excludeIntervals
label: excludeIntervals
doc: '(-XLOne) This argument may be specified 0 or more times. Default value: null. '
type:
- boolean
- 'null'
inputBinding:
prefix: --exclude-intervals
- id: f1r2MaxDepth
label: f1r2MaxDepth
doc: 'sites with depth higher than this value will be grouped Default value: 200.'
type:
- int
- 'null'
inputBinding:
prefix: --f1r2-max-depth
- id: f1r2MedianMq
label: f1r2MedianMq
doc: 'skip sites with median mapping quality below this value Default value: 50.'
type:
- int
- 'null'
inputBinding:
prefix: --f1r2-median-mq
- id: f1r2MinBq
label: f1r2MinBq
doc: 'exclude bases below this quality from pileup Default value: 20.'
type:
- int
- 'null'
inputBinding:
prefix: --f1r2-min-bq
- id: f1r2TarGz_outputFilename
label: f1r2TarGz_outputFilename
doc: |-
If specified, collect F1R2 counts and output files into this tar.gz file Default value: null.
type:
- string
- 'null'
default: generated.tar.gz
inputBinding:
prefix: --f1r2-tar-gz
- id: founderId
label: founderId
doc: |-
(--founder-id) Samples representing the population founders This argument may be specified 0 or more times. Default value: null.
type:
- string
- 'null'
inputBinding:
prefix: -founder-id
- id: gatkConfigFile
label: gatkConfigFile
doc: 'A configuration file to use with the GATK. Default value: null.'
type:
- string
- 'null'
inputBinding:
prefix: --gatk-config-file
- id: gcsRetries
label: gcsRetries
doc: |-
(--gcs-max-retries) If the GCS bucket channel errors out, how many times it will attempt to re-initiate the connection Default value: 20.
type:
- int
- 'null'
inputBinding:
prefix: -gcs-retries
- id: gcsProjectForRequesterPays
label: gcsProjectForRequesterPays
doc: |2-
Project to bill when accessing requester pays buckets. If unset, these buckets cannot be accessed. Default value: .
type:
- string
- 'null'
inputBinding:
prefix: --gcs-project-for-requester-pays
- id: genotypeGermlineSites
label: genotypeGermlineSites
doc: |2-
(EXPERIMENTAL) Call all apparent germline site even though they will ultimately be filtered. Default value: false. Possible values: {true, false}
type:
- boolean
- 'null'
inputBinding:
prefix: --genotype-germline-sites
- id: genotypePonSites
label: genotypePonSites
doc: |-
Call sites in the PoN even though they will ultimately be filtered. Default value: false. Possible values: {true, false}
type:
- boolean
- 'null'
inputBinding:
prefix: --genotype-pon-sites
- id: germlineResource
label: germlineResource
doc: |2-
Population vcf of germline sequencing containing allele fractions. Default value: null.
type:
- File
- 'null'
secondaryFiles:
- pattern: .tbi
inputBinding:
prefix: --germline-resource
- id: graph
label: graph
doc: |-
(--graph-output) Write debug assembly graph information to this file Default value: null.
type:
- string
- 'null'
inputBinding:
prefix: -graph
- id: help
label: help
doc: |-
(--help) display the help message Default value: false. Possible values: {true, false}
type:
- boolean
- 'null'
inputBinding:
prefix: -h
- id: ignoreItrArtifacts
label: ignoreItrArtifacts
doc: ' inverted tandem repeats. Default value: false. Possible values: {true, false} '
type:
- string
- 'null'
inputBinding:
prefix: --ignore-itr-artifactsTurn
- id: initialTumorLod
label: initialTumorLod
doc: |-
(-init-lod) Log 10 odds threshold to consider pileup active. Default value: 2.0.
type:
- string
- 'null'
inputBinding:
prefix: --initial-tumor-lod
- id: intervalExclusionPadding
label: intervalExclusionPadding
doc: |-
(-ixp) Amount of padding (in bp) to add to each interval you are excluding. Default value: 0.
type:
- string
- 'null'
inputBinding:
prefix: --interval-exclusion-padding
- id: imr
label: imr
doc: |-
(--interval-merging-rule) Interval merging rule for abutting intervals Default value: ALL. Possible values: {ALL, OVERLAPPING_ONLY}
type:
- string
- 'null'
inputBinding:
prefix: --interval-merging-rule
- id: ip
label: ip
doc: '(--interval-padding) Default value: 0.'
type:
- string
- 'null'
inputBinding:
prefix: -ipAmount
- id: isr
label: isr
doc: |-
(--interval-set-rule) Set merging approach to use for combining interval inputs Default value: UNION. Possible values: {UNION, INTERSECTION}
type:
- string
- 'null'
inputBinding:
prefix: --interval-set-rule
- id: intervals
label: intervals
doc: |-
(-L) One or more genomic intervals over which to operate This argument may be specified 0 or more times. Default value: null.
type:
- File
- 'null'
inputBinding:
prefix: --intervals
- id: le
label: le
doc: |-
(--lenient) Lenient processing of VCF files Default value: false. Possible values: {true, false}
type:
- boolean
- 'null'
inputBinding:
prefix: -LE
- id: maxPopulationAf
label: maxPopulationAf
doc: |-
(-max-af) Maximum population allele frequency in tumor-only mode. Default value: 0.01.
type:
- string
- 'null'
inputBinding:
prefix: --max-population-af
- id: maxReadsPerAlignmentStart
label: maxReadsPerAlignmentStart
doc: |2-
Maximum number of reads to retain per alignment start position. Reads above this threshold will be downsampled. Set to 0 to disable. Default value: 50.
type:
- int
- 'null'
inputBinding:
prefix: --max-reads-per-alignment-start
- id: minBaseQualityScore
label: minBaseQualityScore
doc: |-
(-mbq:Byte) Minimum base quality required to consider a base for calling Default value: 10.
type:
- string
- 'null'
inputBinding:
prefix: --min-base-quality-score
- id: mitochondriaMode
label: mitochondriaMode
doc: |-
Mitochondria mode sets emission and initial LODs to 0. Default value: false. Possible values: {true, false}
type:
- boolean
- 'null'
inputBinding:
prefix: --mitochondria-mode
- id: nativePairHmmThreads
label: nativePairHmmThreads
doc: ' How many threads should a native pairHMM implementation use Default value:
4. '
type:
- int
- 'null'
inputBinding:
prefix: --native-pair-hmm-threads
valueFrom: |-
$([inputs.runtime_cpu, 4, 1].filter(function (inner) { return inner != null })[0])
- id: nativePairHmmUseDoublePrecision
label: nativePairHmmUseDoublePrecision
doc: |2-
use double precision in the native pairHmm. This is slower but matches the java implementation better Default value: false. Possible values: {true, false}
type:
- boolean
- 'null'
inputBinding:
prefix: --native-pair-hmm-use-double-precision
- id: normalLod
label: normalLod
doc: |-
Log 10 odds threshold for calling normal variant non-germline. Default value: 2.2.
type:
- double
- 'null'
inputBinding:
prefix: --normal-lod
- id: encode
label: encode
doc: 'This argument may be specified 0 or more times. Default value: null.'
type:
- string
- 'null'
inputBinding:
prefix: -encode
- id: panelOfNormals
label: panelOfNormals
doc: |-
(--panel-of-normals) VCF file of sites observed in normal. Default value: null.
type:
- File
- 'null'
secondaryFiles:
- pattern: .tbi
inputBinding:
prefix: --panel-of-normals
- id: pcrIndelQual
label: pcrIndelQual
doc: 'Phred-scaled PCR SNV qual for overlapping fragments Default value: 40.'
type:
- int
- 'null'
inputBinding:
prefix: --pcr-indel-qual
- id: pcrSnvQual
label: pcrSnvQual
doc: 'Phred-scaled PCR SNV qual for overlapping fragments Default value: 40.'
type:
- int
- 'null'
inputBinding:
prefix: --pcr-snv-qual
- id: pedigree
label: pedigree
doc: |-
(-ped) Pedigree file for determining the population founders. Default value: null.
type:
- string
- 'null'
inputBinding:
prefix: --pedigree
- id: quiet
label: quiet
doc: |-
Whether to suppress job-summary info on System.err. Default value: false. Possible values: {true, false}
type:
- boolean
- 'null'
inputBinding:
prefix: --QUIET
- id: readFilter
label: readFilter
doc: |-
(-RF) Read filters to be applied before analysis This argument may be specified 0 or more times. Default value: null. Possible Values: {AlignmentAgreesWithHeaderReadFilter, AllowAllReadsReadFilter, AmbiguousBaseReadFilter, CigarContainsNoNOperator, FirstOfPairReadFilter, FragmentLengthReadFilter, GoodCigarReadFilter, HasReadGroupReadFilter, IntervalOverlapReadFilter, LibraryReadFilter, MappedReadFilter, MappingQualityAvailableReadFilter, MappingQualityNotZeroReadFilter, MappingQualityReadFilter, MatchingBasesAndQualsReadFilter, MateDifferentStrandReadFilter, MateOnSameContigOrNoMappedMateReadFilter, MateUnmappedAndUnmappedReadFilter, MetricsReadFilter, NonChimericOriginalAlignmentReadFilter, NonZeroFragmentLengthReadFilter, NonZeroReferenceLengthAlignmentReadFilter, NotDuplicateReadFilter, NotOpticalDuplicateReadFilter, NotSecondaryAlignmentReadFilter, NotSupplementaryAlignmentReadFilter, OverclippedReadFilter, PairedReadFilter, PassesVendorQualityCheckReadFilter, PlatformReadFilter, PlatformUnitReadFilter, PrimaryLineReadFilter, ProperlyPairedReadFilter, ReadGroupBlackListReadFilter, ReadGroupReadFilter, ReadLengthEqualsCigarLengthReadFilter, ReadLengthReadFilter, ReadNameReadFilter, ReadStrandFilter, SampleReadFilter, SecondOfPairReadFilter, SeqIsStoredReadFilter, ValidAlignmentEndReadFilter, ValidAlignmentStartReadFilter, WellformedReadFilter}
type:
- string
- 'null'
inputBinding:
prefix: --read-filter
- id: readIndex
label: readIndex
doc: |-
(--read-index) Indices to use for the read inputs. If specified, an index must be provided for every read input and in the same order as the read inputs. If this argument is not specified, the path to the index for each input will be inferred automatically. This argument may be specified 0 or more times. Default value: null.
type:
- string
- 'null'
inputBinding:
prefix: -read-index
- id: readValidationStringency
label: readValidationStringency
doc: |-
(-VS:ValidationStringency) Validation stringency for all SAM/BAM/CRAM/SRA files read by this program. The default stringency value SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded. Default value: SILENT. Possible values: {STRICT, LENIENT, SILENT}
type:
- string
- 'null'
inputBinding:
prefix: --read-validation-stringency
- id: secondsBetweenProgressUpdates
label: secondsBetweenProgressUpdates
doc: |-
(--seconds-between-progress-updates) Output traversal statistics every time this many seconds elapse Default value: 10.0.
type:
- double
- 'null'
inputBinding:
prefix: -seconds-between-progress-updates
- id: sequenceDictionary
label: sequenceDictionary
doc: |-
(--sequence-dictionary) Use the given sequence dictionary as the master/canonical sequence dictionary. Must be a .dict file. Default value: null.
type:
- string
- 'null'
inputBinding:
prefix: -sequence-dictionary
- id: sitesOnlyVcfOutput
label: sitesOnlyVcfOutput
doc: |2-
If true, don't emit genotype fields when writing vcf file output. Default value: false. Possible values: {true, false}
type:
- boolean
- 'null'
inputBinding:
prefix: --sites-only-vcf-output
- id: tmpDir
label: tmpDir
doc: 'Temp directory to use. Default value: null.'
type:
- string
- 'null'
inputBinding:
prefix: --tmp-dir
- id: tumorLodToEmit
label: tumorLodToEmit
doc: '(-emit-lod) Log 10 odds threshold to emit variant to VCF. Default value:
3.0. '
type:
- string
- 'null'
inputBinding:
prefix: --tumor-lod-to-emit
- id: tumor
label: tumor
doc: |-
(--tumor-sample) BAM sample name of tumor. May be URL-encoded as output by GetSampleName with -encode argument. Default value: null.
type:
- string
- 'null'
inputBinding:
prefix: -tumor
- id: jdkDeflater
label: jdkDeflater
doc: |-
(--use-jdk-deflater) Whether to use the JdkDeflater (as opposed to IntelDeflater) Default value: false. Possible values: {true, false}
type:
- boolean
- 'null'
inputBinding:
prefix: -jdk-deflater
- id: jdkInflater
label: jdkInflater
doc: |-
(--use-jdk-inflater) Whether to use the JdkInflater (as opposed to IntelInflater) Default value: false. Possible values: {true, false}
type:
- boolean
- 'null'
inputBinding:
prefix: -jdk-inflater
- id: verbosity
label: verbosity
doc: |-
(--verbosity) Control verbosity of logging. Default value: INFO. Possible values: {ERROR, WARNING, INFO, DEBUG}
type:
- string
- 'null'
inputBinding:
prefix: -verbosity
- id: version
label: version
doc: |-
display the version number for this tool Default value: false. Possible values: {true, false}
type:
- boolean
- 'null'
inputBinding:
prefix: --version
- id: activeProbabilityThreshold
label: activeProbabilityThreshold
doc: |2-
Minimum probability for a locus to be considered active. Default value: 0.002.
type:
- double
- 'null'
inputBinding:
prefix: --active-probability-threshold
- id: adaptivePruningInitialErrorRate
label: adaptivePruningInitialErrorRate
doc: ' Initial base error rate estimate for adaptive pruning Default value: 0.001. '
type:
- double
- 'null'
inputBinding:
prefix: --adaptive-pruning-initial-error-rate
- id: allowNonUniqueKmersInRef
label: allowNonUniqueKmersInRef
doc: |2-
Allow graphs that have non-unique kmers in the reference Default value: false. Possible values: {true, false}
type:
- boolean
- 'null'
inputBinding:
prefix: --allow-non-unique-kmers-in-ref
- id: assemblyRegionPadding
label: assemblyRegionPadding
doc: |2-
Number of additional bases of context to include around each assembly region Default value: 100.
type:
- int
- 'null'
inputBinding:
prefix: --assembly-region-padding
- id: bamWriterType
label: bamWriterType
doc: |-
Which haplotypes should be written to the BAM Default value: CALLED_HAPLOTYPES. Possible values: {ALL_POSSIBLE_HAPLOTYPES, CALLED_HAPLOTYPES}
type:
- string
- 'null'
inputBinding:
prefix: --bam-writer-type
- id: debugAssembly
label: debugAssembly
doc: |-
(-debug) Print out verbose debug information about each assembly region Default value: false. Possible values: {true, false}
type:
- string
- 'null'
inputBinding:
prefix: --debug-assembly
- id: disableAdaptivePruning
label: disableAdaptivePruning
doc: |2-
Disable the adaptive algorithm for pruning paths in the graph Default value: false. Possible values: {true, false}
type:
- boolean
- 'null'
inputBinding:
prefix: --disable-adaptive-pruning
- id: disableToolDefaultAnnotations
label: disableToolDefaultAnnotations
doc: |-
(--disable-tool-default-annotations) Disable all tool default annotations Default value: false. Possible values: {true, false}
type:
- boolean
- 'null'
inputBinding:
prefix: -disable-tool-default-annotations
- id: disableToolDefaultReadFilters
label: disableToolDefaultReadFilters
doc: |-
(--disable-tool-default-read-filters) Disable all tool default read filters (WARNING: many tools will not function correctly without their default read filters on) Default value: false. Possible values: {true, false}
type:
- boolean
- 'null'
inputBinding:
prefix: -disable-tool-default-read-filters
- id: dontIncreaseKmerSizesForCycles
label: dontIncreaseKmerSizesForCycles
doc: |2-
Disable iterating over kmer sizes when graph cycles are detected Default value: false. Possible values: {true, false}
type:
- boolean
- 'null'
inputBinding:
prefix: --dont-increase-kmer-sizes-for-cycles
- id: dontTrimActiveRegions
label: dontTrimActiveRegions
doc: |2-
If specified, we will not trim down the active region from the full region (active + extension) to just the active interval for genotyping Default value: false. Possible values: {true, false}
type:
- boolean
- 'null'
inputBinding:
prefix: --dont-trim-active-regions
- id: dontUseSoftClippedBases
label: dontUseSoftClippedBases
doc: |2-
Do not analyze soft clipped bases in the reads Default value: false. Possible values: {true, false}
type:
- boolean
- 'null'
inputBinding:
prefix: --dont-use-soft-clipped-bases
- id: erc
label: erc
doc: |-
(--emit-ref-confidence) (BETA feature) Mode for emitting reference confidence scores Default value: NONE. Possible values: {NONE, BP_RESOLUTION, GVCF}
type:
- string
- 'null'
inputBinding:
prefix: -ERC
- id: enableAllAnnotations
label: enableAllAnnotations
doc: |2-
Use all possible annotations (not for the faint of heart) Default value: false. Possible values: {true, false}
type:
- boolean
- 'null'
inputBinding:
prefix: --enable-all-annotations
- id: forceActive
label: forceActive
doc: |-
If provided, all regions will be marked as active Default value: false. Possible values: {true, false}
type:
- boolean
- 'null'
inputBinding:
prefix: --force-active
- id: genotypeFilteredAlleles
label: genotypeFilteredAlleles
doc: |2-
Whether to force genotype even filtered alleles Default value: false. Possible values: {true, false}
type:
- boolean
- 'null'
inputBinding:
prefix: --genotype-filtered-alleles
- id: gvcfLodBand
label: gvcfLodBand
doc: |-
(-LODB) Exclusive upper bounds for reference confidence LOD bands (must be specified in increasing order) This argument may be specified 0 or more times. Default value: [-2.5, -2.0, -1.5,
type:
- string
- 'null'
inputBinding:
prefix: --gvcf-lod-band
- id: kmerSize
label: kmerSize
doc: |-
Kmer size to use in the read threading assembler This argument may be specified 0 or more times. Default value: [10, 25].
type:
- int
- 'null'
inputBinding:
prefix: --kmer-size
- id: maxAssemblyRegionSize
label: maxAssemblyRegionSize
doc: ' Maximum size of an assembly region Default value: 300. '
type:
- int
- 'null'
inputBinding:
prefix: --max-assembly-region-size
- id: mnpDist
label: mnpDist
doc: |-
(--max-mnp-distance) Two or more phased substitutions separated by this distance or less are merged into MNPs. Default value: 1.
type:
- int
- 'null'
inputBinding:
prefix: -mnp-dist
- id: maxNumHaplotypesInPopulation
label: maxNumHaplotypesInPopulation
doc: |2-
Maximum number of haplotypes to consider for your population Default value: 128.
type:
- int
- 'null'
inputBinding:
prefix: --max-num-haplotypes-in-population
- id: maxProbPropagationDistance
label: maxProbPropagationDistance
doc: |2-
Upper limit on how many bases away probability mass can be moved around when calculating the boundaries between active and inactive assembly regions Default value: 50.
type:
- int
- 'null'
inputBinding:
prefix: --max-prob-propagation-distance
- id: maxSuspiciousReadsPerAlignmentStart
label: maxSuspiciousReadsPerAlignmentStart
doc: |2-
Maximum number of suspicious reads (mediocre mapping quality or too many substitutions) allowed in a downsampling stride. Set to 0 to disable. Default value: 0.
type:
- int
- 'null'
inputBinding:
prefix: --max-suspicious-reads-per-alignment-start
- id: maxUnprunedVariants
label: maxUnprunedVariants
doc: |2-
Maximum number of variants in graph the adaptive pruner will allow Default value: 100.
type:
- int
- 'null'
inputBinding:
prefix: --max-unpruned-variants
- id: minAssemblyRegionSize
label: minAssemblyRegionSize
doc: ' Minimum size of an assembly region Default value: 50. '
type:
- int
- 'null'
inputBinding:
prefix: --min-assembly-region-size
- id: minDanglingBranchLength
label: minDanglingBranchLength
doc: ' Minimum length of a dangling branch to attempt recovery Default value: 4. '
type:
- int
- 'null'
inputBinding:
prefix: --min-dangling-branch-length
- id: minPruning
label: minPruning
doc: 'Minimum support to not prune paths in the graph Default value: 2.'
type:
- int
- 'null'
inputBinding:
prefix: --min-pruning
- id: minimumAlleleFraction
label: minimumAlleleFraction
doc: |-
(-min-AF) Lower bound of variant allele fractions to consider when calculating variant LOD Default value: 0.0.
type:
- float
- 'null'
inputBinding:
prefix: --minimum-allele-fraction
- id: numPruningSamples
label: numPruningSamples
doc: 'Default value: 1.'
type:
- int
- 'null'
inputBinding:
prefix: --num-pruning-samples
- id: pairHmmGapContinuationPenalty
label: pairHmmGapContinuationPenalty
doc: ' Flat gap continuation penalty for use in the Pair HMM Default value: 10. '
type:
- int
- 'null'
inputBinding:
prefix: --pair-hmm-gap-continuation-penalty
- id: pairhmm
label: pairhmm
doc: |-
(--pair-hmm-implementation) The PairHMM implementation to use for genotype likelihood calculations Default value: FASTEST_AVAILABLE. Possible values: {EXACT, ORIGINAL, LOGLESS_CACHING, AVX_LOGLESS_CACHING, AVX_LOGLESS_CACHING_OMP, EXPERIMENTAL_FPGA_LOGLESS_CACHING, FASTEST_AVAILABLE}
type:
- string
- 'null'
inputBinding:
prefix: -pairHMM
- id: pcrIndelModel
label: pcrIndelModel
doc: |2-
The PCR indel model to use Default value: CONSERVATIVE. Possible values: {NONE, HOSTILE, AGGRESSIVE, CONSERVATIVE}
type:
- string
- 'null'
inputBinding:
prefix: --pcr-indel-model
- id: phredScaledGlobalReadMismappingRate
label: phredScaledGlobalReadMismappingRate
doc: ' The global assumed mismapping rate for reads Default value: 45. '
type:
- int
- 'null'
inputBinding:
prefix: --phred-scaled-global-read-mismapping-rate
- id: pruningLodThreshold
label: pruningLodThreshold
doc: 'Default value: 2.302585092994046. '
type:
- float
- 'null'
inputBinding:
prefix: --pruning-lod-thresholdLn
- id: recoverAllDanglingBranches
label: recoverAllDanglingBranches
doc: |2-
Recover all dangling branches Default value: false. Possible values: {true, false}
type:
- boolean
- 'null'
inputBinding:
prefix: --recover-all-dangling-branches
- id: showhidden
label: showhidden
doc: |-
(--showHidden) display hidden arguments Default value: false. Possible values: {true, false}
type:
- boolean
- 'null'
inputBinding:
prefix: -showHidden
- id: smithWaterman
label: smithWaterman
doc: |2-
Which Smith-Waterman implementation to use, generally FASTEST_AVAILABLE is the right choice Default value: JAVA. Possible values: {FASTEST_AVAILABLE, AVX_ENABLED, JAVA}
type:
- string
- 'null'
inputBinding:
prefix: --smith-waterman
- id: ambigFilterBases
label: ambigFilterBases
doc: |-
Threshold number of ambiguous bases. If null, uses threshold fraction; otherwise, overrides threshold fraction. Default value: null. Cannot be used in conjuction with argument(s) maxAmbiguousBaseFraction
type:
- int
- 'null'
inputBinding:
prefix: --ambig-filter-bases
- id: ambigFilterFrac
label: ambigFilterFrac
doc: |-
Threshold fraction of ambiguous bases Default value: 0.05. Cannot be used in conjuction with argument(s) maxAmbiguousBases
type:
- double
- 'null'
inputBinding:
prefix: --ambig-filter-frac
- id: maxFragmentLength
label: maxFragmentLength
doc: 'Default value: 1000000.'
type:
- int
- 'null'
inputBinding:
prefix: --max-fragment-length
- id: minFragmentLength
label: minFragmentLength
doc: 'Default value: 0.'
type:
- int
- 'null'
inputBinding:
prefix: --min-fragment-length
- id: keepIntervals
label: keepIntervals
doc: |-
One or more genomic intervals to keep This argument must be specified at least once. Required.
type:
- string
- 'null'
inputBinding:
prefix: --keep-intervals
- id: library
label: library
doc: |-
(--library) Name of the library to keep This argument must be specified at least once. Required.
type:
- string
- 'null'
inputBinding:
prefix: -library
- id: maximumMappingQuality
label: maximumMappingQuality
doc: ' Maximum mapping quality to keep (inclusive) Default value: null. '
type:
- int
- 'null'
inputBinding:
prefix: --maximum-mapping-quality
- id: minimumMappingQuality
label: minimumMappingQuality
doc: ' Minimum mapping quality to keep (inclusive) Default value: 20. '
type:
- int
- 'null'
inputBinding:
prefix: --minimum-mapping-quality
- id: dontRequireSoftClipsBothEnds
label: dontRequireSoftClipsBothEnds
doc: |2-
Allow a read to be filtered out based on having only 1 soft-clipped block. By default, both ends must have a soft-clipped block, setting this flag requires only 1 soft-clipped block Default value: false. Possible values: {true, false}
type:
- boolean
- 'null'
inputBinding:
prefix: --dont-require-soft-clips-both-ends
- id: filterTooShort
label: filterTooShort
doc: 'Minimum number of aligned bases Default value: 30.'
type:
- int
- 'null'
inputBinding:
prefix: --filter-too-short
- id: platformFilterName
label: platformFilterName
doc: This argument must be specified at least once. Required.
type:
- string
- 'null'
inputBinding:
prefix: --platform-filter-name
- id: blackListedLanes
label: blackListedLanes
doc: |-
Platform unit (PU) to filter out This argument must be specified at least once. Required.
type:
- string
- 'null'
inputBinding:
prefix: --black-listed-lanes
- id: readGroupBlackList
label: readGroupBlackList
doc: 'This argument must be specified at least once. Required. '
type:
- string
- 'null'
inputBinding:
prefix: --read-group-black-listThe
- id: keepReadGroup
label: keepReadGroup
doc: The name of the read group to keep Required.
type:
- string
- 'null'
inputBinding:
prefix: --keep-read-group
- id: maxReadLength
label: maxReadLength
doc: |-
Keep only reads with length at most equal to the specified value Default value: 2147483647.
type:
- int
- 'null'
inputBinding:
prefix: --max-read-length
- id: minReadLength
label: minReadLength
doc: |-
Keep only reads with length at least equal to the specified value Default value: 30.
type:
- int
- 'null'
inputBinding:
prefix: --min-read-length
- id: readName
label: readName
doc: Keep only reads with this read name Required.
type:
- string
- 'null'
inputBinding:
prefix: --read-name
- id: keepReverseStrandOnly
label: keepReverseStrandOnly
doc: |2-
Keep only reads on the reverse strand Required. Possible values: {true, false}
type:
- boolean
- 'null'
inputBinding:
prefix: --keep-reverse-strand-only
- id: sample
label: sample
doc: |-
(--sample) The name of the sample(s) to keep, filtering out all others This argument must be specified at least once. Required.
type:
- string
- 'null'
inputBinding:
prefix: -sample
outputs:
- id: out
label: out
doc: To determine type
type: File
secondaryFiles:
- pattern: .tbi
outputBinding:
glob: '$(inputs.outputPrefix ? inputs.outputPrefix : "generated").vcf.gz'
loadContents: false
- id: stats
label: stats
doc: To determine type
type: File
outputBinding:
glob: $((inputs.outputFilename + ".stats"))
outputEval: $((inputs.outputFilename.basename + ".stats"))
loadContents: false
- id: f1f2r_out
label: f1f2r_out
doc: To determine type
type: File
outputBinding:
glob: generated.tar.gz
loadContents: false
- id: bam
label: bam
doc: File to which assembled haplotypes should be written
type:
- File
- 'null'
secondaryFiles:
- |-
${
function resolveSecondary(base, secPattern) {
if (secPattern[0] == "^") {
var spl = base.split(".");
var endIndex = spl.length > 1 ? spl.length - 1 : 1;
return resolveSecondary(spl.slice(undefined, endIndex).join("."), secPattern.slice(1));
}
return base + secPattern
}
return [
{
path: resolveSecondary(self.path, "^.bai"),
basename: resolveSecondary(self.basename, ".bai"),
class: "File",
}
];
}
outputBinding:
glob: '$(inputs.outputBamName ? inputs.outputBamName : "generated")'
loadContents: false
stdout: _stdout
stderr: _stderr
baseCommand:
- gatk
- Mutect2
arguments:
- prefix: --java-options
position: -1
valueFrom: |-
$("-Xmx{memory}G {compression} {otherargs}".replace(/\{memory\}/g, (([inputs.runtime_memory, 16, 4].filter(function (inner) { return inner != null })[0] * 3) / 4)).replace(/\{compression\}/g, (inputs.compression_level != null) ? ("-Dsamjdk.compress_level=" + inputs.compression_level) : "").replace(/\{otherargs\}/g, [inputs.javaOptions, []].filter(function (inner) { return inner != null })[0].join(" ")))
hints:
- class: ToolTimeLimit
timelimit: |-
$([inputs.runtime_seconds, 86400].filter(function (inner) { return inner != null })[0])
id: Gatk4Mutect2