GATK4: SelectVariants¶
Gatk4SelectVariants
· 1 contributor · 4 versions
USAGE: Selectvariants [arguments] This tool makes it possible to select a subset of variants based on various criteria in order to facilitate certain analyses. Examples include comparing and contrasting cases vs. controls, extracting variant or non-variant loci that meet certain requirements, or troubleshooting some unexpected results, to name a few. Version:4.1.3.0
Quickstart¶
from janis_bioinformatics.tools.gatk4.selectvariants.versions import Gatk4SelectVariants_4_1_4 wf = WorkflowBuilder("myworkflow") wf.step( "gatk4selectvariants_step", Gatk4SelectVariants_4_1_4( ) ) wf.output("out", source=gatk4selectvariants_step.out)
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 Gatk4SelectVariants:
# user inputs
janis inputs Gatk4SelectVariants > inputs.yaml
inputs.yaml
{}
- Run Gatk4SelectVariants with:
janis run [...run options] \
--inputs inputs.yaml \
Gatk4SelectVariants
Information¶
ID: | Gatk4SelectVariants |
---|---|
URL: | No URL to the documentation was provided |
Versions: | 4.1.4.0, 4.1.3.0, 4.1.2.0, 4.0.12.0 |
Container: | broadinstitute/gatk:4.1.4.0 |
Authors: | Sebastian Hollizeck |
Citations: | None |
Created: | 2019-12-02 |
Updated: | 2019-12-02 |
Outputs¶
name | type | documentation |
---|---|---|
out | Gzipped<VCF> |
Additional configuration (inputs)¶
name | type | prefix | position | documentation |
---|---|---|---|---|
javaOptions | Optional<Array<String>> | |||
compression_level | Optional<Integer> | Compression level for all compressed files created (e.g. BAM and VCF). Default value: 2. | ||
outputFilename | Optional<Filename> | -O | (–output) Required. | |
variants | Optional<Gzipped<VCF>> | -V | (–variant) A VCF file containing variants Required. | |
addOutputSamProgramRecord | Optional<Boolean> | -add-output-sam-program-record:Boolean | (–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} | |
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. | |
cloudIndexPrefetchBuffer | Optional<Integer> | –cloud-index-prefetch-buffer | (-CIPB:Integer) 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:Integer) Size of the cloud-only prefetch buffer (in MB; 0 to disable). Default value: 40. | |
conc | Optional<String> | -conc | (–concordance) Output variants also called in this comparison track Default value: null. | |
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:Boolean) 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<String> | –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: {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} | |
disc | Optional<String> | -disc | (–discordance) Output variants not called in this comparison track Default value: null. | |
dropGenotypeAnnotation | Optional<String> | –drop-genotype-annotation | (-DGA:String) Genotype annotations to drop from output vcf. Annotations to be dropped are specified by their key. This argument may be specified 0 or more times. Default value: null. | |
dropInfoAnnotation | Optional<String> | –drop-info-annotation | (-DA:String) Info annotations to drop from output vcf. Annotations to be dropped are specified by their key. This argument may be specified 0 or more times. Default value: null. | |
excludeFiltered | Optional<Boolean> | –exclude-filtered | Don’t include filtered sites Default value: false. Possible values: {true, false} | |
xlIds | Optional<String> | -xl-ids | (–exclude-ids) List of variant rsIDs to exclude This argument may be specified 0 or more times. Default value: null. | |
excludeIntervals | Optional<String> | –exclude-intervals | (-XL) This argument may be specified 0 or more times. Default value: null. | |
excludeNonvariants | Optional<String> | –exclude-non-variants | Default value: false. Possible values: {true, false} | |
excludeSampleExpressions | Optional<String> | –exclude-sample-expressions | (-xl-se:String) List of sample expressions to exclude This argument may be specified 0 or more times. Default value: null. | |
excludeSampleName | Optional<String> | –exclude-sample-name | (-xl-sn:String) Exclude genotypes from this sample This argument may be specified 0 or more times. Default value: null. | |
gatkConfigFile | Optional<File> | –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: . | |
help | Optional<Boolean> | -h | (–help) display the help message Default value: false. Possible values: {true, false} | |
bam | Optional<IndexedBam> | -I | (–input) BAM/SAM/CRAM file containing reads This argument may be specified 0 or more times. Default value: null. | |
intervalExclusionPadding | Optional<Integer> | –interval-exclusion-padding | (-ixp:Integer) Amount of padding (in bp) to add to each interval you are excluding. Default value: 0. | |
imr | Optional<String> | -imr | (–interval-merging-rule) Interval merging rule for abutting intervals Default value: ALL. Possible values: {ALL, OVERLAPPING_ONLY} | |
ip | Optional<Integer> | -ip | (–interval-padding) Default value: 0. | |
isr | Optional<String> | -isr | (–interval-set-rule) Set merging approach to use for combining interval inputs Default value: UNION. Possible values: {UNION, INTERSECTION} | |
intervals | Optional<String> | –intervals | (-L:String) One or more genomic intervals over which to operate This argument may be specified 0 or more times. Default value: null. | |
invertMendelianViolation | Optional<Boolean> | –invert-mendelian-violation | Output non-mendelian violation sites only Default value: false. Possible values: {true, false} | |
invertSelect | Optional<Boolean> | -invert-select | (–invertSelect) Invert the selection criteria for -select Default value: false. Possible values: {true, false} | |
ids | Optional<String> | -ids | (–keep-ids) List of variant rsIDs to select This argument may be specified 0 or more times. Default value: null. | |
keepOriginalAc | Optional<Boolean> | –keep-original-ac | Store the original AC, AF, and AN values after subsetting Default value: false. Possible values: {true, false} | |
keepOriginalDp | Optional<Boolean> | –keep-original-dp | Store the original DP value after subsetting Default value: false. Possible values: {true, false} | |
le | Optional<Boolean> | -LE | (–lenient) Lenient processing of VCF files Default value: false. Possible values: {true, false} | |
maxFilteredGenotypes | Optional<Integer> | –max-filtered-genotypes | Maximum number of samples filtered at the genotype level Default value: 2147483647. | |
maxFractionFilteredGenotypes | Optional<Double> | –max-fraction-filtered-genotypes | Maximum fraction of samples filtered at the genotype level Default value: 1.0. | |
maxIndelSize | Optional<Integer> | –max-indel-size | Maximum size of indels to include Default value: 2147483647. | |
maxNocallFraction | Optional<Double> | –max-nocall-fraction | Maximum fraction of samples with no-call genotypes Default value: 1.0. | |
maxNocallNumber | Optional<Integer> | –max-nocall-number | Maximum number of samples with no-call genotypes Default value: 2147483647. | |
mendelianViolation | Optional<Boolean> | –mendelian-violation | Default value: false. Possible values: {true, false} | |
mendelianViolationQualThreshold | Optional<Double> | –mendelian-violation-qual-threshold | Minimum GQ score for each trio member to accept a site as a violation Default value: 0.0. | |
minFilteredGenotypes | Optional<Integer> | –min-filtered-genotypes | Minimum number of samples filtered at the genotype level Default value: 0. | |
minFractionFilteredGenotypes | Optional<Double> | –min-fraction-filtered-genotypes | Maximum fraction of samples filtered at the genotype level Default value: 0.0. | |
minIndelSize | Optional<Integer> | –min-indel-size | Minimum size of indels to include Default value: 0. | |
pedigree | Optional<File> | –pedigree | (-ped:File) Pedigree file Default value: null. | |
preserveAlleles | Optional<Boolean> | –preserve-alleles | Preserve original alleles, do not trim Default value: false. Possible values: {true, false} | |
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:String) 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, SoftClippedReadFilter, ValidAlignmentEndReadFilter, ValidAlignmentStartReadFilter, WellformedReadFilter} | |
readIndex | Optional<File> | -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} | |
reference | Optional<FastaWithIndexes> | –reference | (-R:String) Reference sequence Default value: null. | |
removeFractionGenotypes | Optional<Double> | –remove-fraction-genotypes | Select a fraction of genotypes at random from the input and sets them to no-call Default value: 0.0. | |
removeUnusedAlternates | Optional<Boolean> | –remove-unused-alternates | Remove alternate alleles not present in any genotypes Default value: false. Possible values: {true, false} | |
restrictAllelesTo | Optional<String> | –restrict-alleles-to | Select only variants of a particular allelicity Default value: ALL. Possible values: {ALL, BIALLELIC, MULTIALLELIC} | |
sampleExpressions | Optional<String> | –sample-expressions | (-se:String) Regular expression to select multiple samples This argument may be specified 0 or more times. Default value: null. | |
sampleName | Optional<String> | –sample-name | (-sn:String) Include genotypes from this sample This argument may be specified 0 or more times. Default value: null. | |
secondsBetweenProgressUpdates | Optional<Double> | -seconds-between-progress-updates | (–seconds-between-progress-updates) Output traversal statistics every time this many seconds elapse Default value: 10.0. | |
selectRandomFraction | Optional<String> | –select-random-fraction | (-fraction:Double) Select a fraction of variants at random from the input Default value: 0.0. | |
selectTypeToExclude | Optional<String> | –select-type-to-exclude | (-xl-select-type:Type) Do not select certain type of variants from the input file This argument may be specified 0 or more times. Default value: null. Possible values: {NO_VARIATION, SNP, MNP, INDEL, SYMBOLIC, MIXED} | |
selectTypeToInclude | Optional<String> | –select-type-to-include | (-select-type:Type) Select only a certain type of variants from the input file This argument may be specified 0 or more times. Default value: null. Possible values: {NO_VARIATION, SNP, MNP, INDEL, SYMBOLIC, MIXED} | |
selectexpressions | Optional<String> | –selectExpressions | (-select:String) One or more criteria to use when selecting the data This argument may be specified 0 or more times. Default value: null. | |
sequenceDictionary | Optional<File> | -sequence-dictionary | (–sequence-dictionary) Use the given sequence dictionary as the master/canonical sequence dictionary. Must be a .dict file. Default value: null. | |
setFilteredGtToNocall | Optional<Boolean> | –set-filtered-gt-to-nocall | Set filtered genotypes to no-call Default value: false. Possible values: {true, false} | |
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<Filename> | –tmp-dir | Temp directory to use. 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} | |
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} | |
showhidden | Optional<Boolean> | -showHidden | (–showHidden) display hidden arguments Default value: false. Possible values: {true, false} | |
ambigFilterBases | Optional<Integer> | –ambig-filter-bases | Valid only if ‘AmbiguousBaseReadFilter’ is specified: 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 | Valid only if ‘AmbiguousBaseReadFilter’ is specified: Threshold fraction of ambiguous bases Default value: 0.05. Cannot be used in conjuction with argument(s) maxAmbiguousBases | |
maxFragmentLength | Optional<Integer> | –max-fragment-length | Valid only if ‘FragmentLengthReadFilter’ is specified: Maximum length of fragment (insert size) Default value: 1000000. | |
minFragmentLength | Optional<Integer> | –min-fragment-length | Valid only if ‘FragmentLengthReadFilter’ is specified: Minimum length of fragment (insert size) Default value: 0. | |
keepIntervals | Optional<String> | –keep-intervals | Valid only if ‘IntervalOverlapReadFilter’ is specified: One or more genomic intervals to keep This argument must be specified at least once. Required. | |
library | Optional<String> | -library | Valid only if ‘LibraryReadFilter’ is specified: (–library) Name of the library to keep This argument must be specified at least once. Required. | |
maximumMappingQuality | Optional<Integer> | –maximum-mapping-quality | Valid only if ‘MappingQualityReadFilter’ is specified: Maximum mapping quality to keep (inclusive) Default value: null. | |
minimumMappingQuality | Optional<Integer> | –minimum-mapping-quality | Valid only if ‘MappingQualityReadFilter’ is specified: Minimum mapping quality to keep (inclusive) Default value: 10. | |
dontRequireSoftClipsBothEnds | Optional<Boolean> | –dont-require-soft-clips-both-ends | Valid only if ‘OverclippedReadFilter’ is specified: 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 | Valid only if ‘OverclippedReadFilter’ is specified: Minimum number of aligned bases Default value: 30. | |
platformFilterName | Optional<String> | –platform-filter-name | Valid only if ‘PlatformReadFilter’ is specified: This argument must be specified at least once. Required. | |
blackListedLanes | Optional<String> | –black-listed-lanes | Valid only if ‘PlatformUnitReadFilter’ is specified: Platform unit (PU) to filter out This argument must be specified at least once. Required. | |
readGroupBlackList | Optional<String> | –read-group-black-list | Valid only if ‘ReadGroupBlackListReadFilter’ is specified: The name of the read group to filter out. This argument must be specified at least once. Required. | |
keepReadGroup | Optional<String> | –keep-read-group | Valid only if ‘ReadGroupReadFilter’ is specified: The name of the read group to keep Required. | |
maxReadLength | Optional<Integer> | –max-read-length | Valid only if ‘ReadLengthReadFilter’ is specified: Keep only reads with length at most equal to the specified value Required. | |
minReadLength | Optional<Integer> | –min-read-length | Valid only if ‘ReadLengthReadFilter’ is specified: Keep only reads with length at least equal to the specified value Default value: 1. | |
readName | Optional<String> | –read-name | Valid only if ‘ReadNameReadFilter’ is specified: Keep only reads with this read name Required. | |
keepReverseStrandOnly | Optional<Boolean> | –keep-reverse-strand-only | Valid only if ‘ReadStrandFilter’ is specified: Keep only reads on the reverse strand Required. Possible values: {true, false} | |
sample | Optional<String> | –sample | Valid only if ‘SampleReadFilter’ is specified: The name of the sample(s) to keep, filtering out all others This argument must be specified at least once. Required. | |
invertSoftClipRatioFilter | Optional<Boolean> | –invert-soft-clip-ratio-filter | Inverts the results from this filter, causing all variants that would pass to fail and visa-versa. Default value: false. Possible values: {true, false} | |
softClippedLeadingTrailingRatio | Optional<Double> | –soft-clipped-leading-trailing-ratio | Threshold ratio of soft clipped bases (leading / trailing the cigar string) to total bases in read for read to be filtered. Default value: null. Cannot be used in conjuction with argument(s) minimumSoftClippedRatio | |
softClippedRatioThreshold | Optional<Double> | –soft-clipped-ratio-threshold | Threshold ratio of soft clipped bases (anywhere in the cigar string) to total bases in read for read to be filtered. Default value: null. Cannot be used in conjuction with argument(s) minimumLeadingTrailingSoftClippedRatio |
Workflow Description Language¶
version development
task Gatk4SelectVariants {
input {
Int? runtime_cpu
Int? runtime_memory
Int? runtime_seconds
Int? runtime_disks
Array[String]? javaOptions
Int? compression_level
String? outputFilename
File? variants
File? variants_tbi
Boolean? addOutputSamProgramRecord
Boolean? addOutputVcfCommandLine
File? arguments_file
Int? cloudIndexPrefetchBuffer
Int? cloudPrefetchBuffer
String? conc
Boolean? createOutputBamIndex
Boolean? createOutputBamMd5
Boolean? createOutputvariantIndex
Boolean? createOutputvariantMd5
Boolean? disableBamIndexCaching
String? disableReadFilter
Boolean? disableSequenceDictionaryValidation
String? disc
String? dropGenotypeAnnotation
String? dropInfoAnnotation
Boolean? excludeFiltered
String? xlIds
String? excludeIntervals
String? excludeNonvariants
String? excludeSampleExpressions
String? excludeSampleName
File? gatkConfigFile
Int? gcsRetries
String? gcsProjectForRequesterPays
Boolean? help
File? bam
File? bam_bai
Int? intervalExclusionPadding
String? imr
Int? ip
String? isr
String? intervals
Boolean? invertMendelianViolation
Boolean? invertSelect
String? ids
Boolean? keepOriginalAc
Boolean? keepOriginalDp
Boolean? le
Int? maxFilteredGenotypes
Float? maxFractionFilteredGenotypes
Int? maxIndelSize
Float? maxNocallFraction
Int? maxNocallNumber
Boolean? mendelianViolation
Float? mendelianViolationQualThreshold
Int? minFilteredGenotypes
Float? minFractionFilteredGenotypes
Int? minIndelSize
File? pedigree
Boolean? preserveAlleles
Boolean? quiet
String? readFilter
File? readIndex
String? readValidationStringency
File? reference
File? reference_fai
File? reference_amb
File? reference_ann
File? reference_bwt
File? reference_pac
File? reference_sa
File? reference_dict
Float? removeFractionGenotypes
Boolean? removeUnusedAlternates
String? restrictAllelesTo
String? sampleExpressions
String? sampleName
Float? secondsBetweenProgressUpdates
String? selectRandomFraction
String? selectTypeToExclude
String? selectTypeToInclude
String? selectexpressions
File? sequenceDictionary
Boolean? setFilteredGtToNocall
Boolean? sitesOnlyVcfOutput
String? tmpDir
Boolean? jdkDeflater
Boolean? jdkInflater
String? verbosity
Boolean? version
Boolean? disableToolDefaultReadFilters
Boolean? showhidden
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
Boolean? invertSoftClipRatioFilter
Float? softClippedLeadingTrailingRatio
Float? softClippedRatioThreshold
}
command <<<
set -e
gatk SelectVariants \
--java-options '-Xmx~{((select_first([runtime_memory, 4]) * 3) / 4)}G ~{if (defined(compression_level)) then ("-Dsamjdk.compress_level=" + compression_level) else ""} ~{sep(" ", select_first([javaOptions, []]))}' \
-O '~{select_first([outputFilename, "generated"])}' \
~{if defined(variants) then ("-V '" + variants + "'") else ""} \
~{if (defined(addOutputSamProgramRecord) && select_first([addOutputSamProgramRecord])) then "-add-output-sam-program-record:Boolean" else ""} \
~{if (defined(addOutputVcfCommandLine) && select_first([addOutputVcfCommandLine])) then "-add-output-vcf-command-line" else ""} \
~{if defined(arguments_file) then ("--arguments_file '" + arguments_file + "'") else ""} \
~{if defined(cloudIndexPrefetchBuffer) then ("--cloud-index-prefetch-buffer " + cloudIndexPrefetchBuffer) else ''} \
~{if defined(cloudPrefetchBuffer) then ("--cloud-prefetch-buffer " + cloudPrefetchBuffer) else ''} \
~{if defined(conc) then ("-conc '" + conc + "'") 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 select_first([createOutputvariantIndex, true]) 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) then ("--disable-read-filter '" + disableReadFilter + "'") else ""} \
~{if (defined(disableSequenceDictionaryValidation) && select_first([disableSequenceDictionaryValidation])) then "-disable-sequence-dictionary-validation" else ""} \
~{if defined(disc) then ("-disc '" + disc + "'") else ""} \
~{if defined(dropGenotypeAnnotation) then ("--drop-genotype-annotation '" + dropGenotypeAnnotation + "'") else ""} \
~{if defined(dropInfoAnnotation) then ("--drop-info-annotation '" + dropInfoAnnotation + "'") else ""} \
~{if (defined(excludeFiltered) && select_first([excludeFiltered])) then "--exclude-filtered" else ""} \
~{if defined(xlIds) then ("-xl-ids '" + xlIds + "'") else ""} \
~{if defined(excludeIntervals) then ("--exclude-intervals '" + excludeIntervals + "'") else ""} \
~{if defined(excludeNonvariants) then ("--exclude-non-variants '" + excludeNonvariants + "'") else ""} \
~{if defined(excludeSampleExpressions) then ("--exclude-sample-expressions '" + excludeSampleExpressions + "'") else ""} \
~{if defined(excludeSampleName) then ("--exclude-sample-name '" + excludeSampleName + "'") 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(help) && select_first([help])) then "-h" else ""} \
~{if defined(bam) then ("-I '" + bam + "'") else ""} \
~{if defined(intervalExclusionPadding) then ("--interval-exclusion-padding " + intervalExclusionPadding) else ''} \
~{if defined(imr) then ("-imr '" + imr + "'") else ""} \
~{if defined(ip) then ("-ip " + ip) else ''} \
~{if defined(isr) then ("-isr '" + isr + "'") else ""} \
~{if defined(intervals) then ("--intervals '" + intervals + "'") else ""} \
~{if (defined(invertMendelianViolation) && select_first([invertMendelianViolation])) then "--invert-mendelian-violation" else ""} \
~{if (defined(invertSelect) && select_first([invertSelect])) then "-invert-select" else ""} \
~{if defined(ids) then ("-ids '" + ids + "'") else ""} \
~{if (defined(keepOriginalAc) && select_first([keepOriginalAc])) then "--keep-original-ac" else ""} \
~{if (defined(keepOriginalDp) && select_first([keepOriginalDp])) then "--keep-original-dp" else ""} \
~{if (defined(le) && select_first([le])) then "-LE" else ""} \
~{if defined(maxFilteredGenotypes) then ("--max-filtered-genotypes " + maxFilteredGenotypes) else ''} \
~{if defined(maxFractionFilteredGenotypes) then ("--max-fraction-filtered-genotypes " + maxFractionFilteredGenotypes) else ''} \
~{if defined(maxIndelSize) then ("--max-indel-size " + maxIndelSize) else ''} \
~{if defined(maxNocallFraction) then ("--max-nocall-fraction " + maxNocallFraction) else ''} \
~{if defined(maxNocallNumber) then ("--max-nocall-number " + maxNocallNumber) else ''} \
~{if (defined(mendelianViolation) && select_first([mendelianViolation])) then "--mendelian-violation" else ""} \
~{if defined(mendelianViolationQualThreshold) then ("--mendelian-violation-qual-threshold " + mendelianViolationQualThreshold) else ''} \
~{if defined(minFilteredGenotypes) then ("--min-filtered-genotypes " + minFilteredGenotypes) else ''} \
~{if defined(minFractionFilteredGenotypes) then ("--min-fraction-filtered-genotypes " + minFractionFilteredGenotypes) else ''} \
~{if defined(minIndelSize) then ("--min-indel-size " + minIndelSize) else ''} \
~{if defined(pedigree) then ("--pedigree '" + pedigree + "'") else ""} \
~{if (defined(preserveAlleles) && select_first([preserveAlleles])) then "--preserve-alleles" 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(reference) then ("--reference '" + reference + "'") else ""} \
~{if defined(removeFractionGenotypes) then ("--remove-fraction-genotypes " + removeFractionGenotypes) else ''} \
~{if (defined(removeUnusedAlternates) && select_first([removeUnusedAlternates])) then "--remove-unused-alternates" else ""} \
~{if defined(restrictAllelesTo) then ("--restrict-alleles-to '" + restrictAllelesTo + "'") else ""} \
~{if defined(sampleExpressions) then ("--sample-expressions '" + sampleExpressions + "'") else ""} \
~{if defined(sampleName) then ("--sample-name '" + sampleName + "'") else ""} \
~{if defined(secondsBetweenProgressUpdates) then ("-seconds-between-progress-updates " + secondsBetweenProgressUpdates) else ''} \
~{if defined(selectRandomFraction) then ("--select-random-fraction '" + selectRandomFraction + "'") else ""} \
~{if defined(selectTypeToExclude) then ("--select-type-to-exclude '" + selectTypeToExclude + "'") else ""} \
~{if defined(selectTypeToInclude) then ("--select-type-to-include '" + selectTypeToInclude + "'") else ""} \
~{if defined(selectexpressions) then ("--selectExpressions '" + selectexpressions + "'") else ""} \
~{if defined(sequenceDictionary) then ("-sequence-dictionary '" + sequenceDictionary + "'") else ""} \
~{if (defined(setFilteredGtToNocall) && select_first([setFilteredGtToNocall])) then "--set-filtered-gt-to-nocall" else ""} \
~{if (defined(sitesOnlyVcfOutput) && select_first([sitesOnlyVcfOutput])) then "--sites-only-vcf-output" else ""} \
--tmp-dir '~{select_first([tmpDir, "generated"])}' \
~{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(disableToolDefaultReadFilters) && select_first([disableToolDefaultReadFilters])) then "-disable-tool-default-read-filters" else ""} \
~{if (defined(showhidden) && select_first([showhidden])) then "-showHidden" 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-list '" + 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 ""} \
~{if (defined(invertSoftClipRatioFilter) && select_first([invertSoftClipRatioFilter])) then "--invert-soft-clip-ratio-filter" else ""} \
~{if defined(softClippedLeadingTrailingRatio) then ("--soft-clipped-leading-trailing-ratio " + softClippedLeadingTrailingRatio) else ''} \
~{if defined(softClippedRatioThreshold) then ("--soft-clipped-ratio-threshold " + softClippedRatioThreshold) else ''}
>>>
runtime {
cpu: select_first([runtime_cpu, 1])
disks: "local-disk ~{select_first([runtime_disks, 20])} SSD"
docker: "broadinstitute/gatk:4.1.4.0"
duration: select_first([runtime_seconds, 86400])
memory: "~{select_first([runtime_memory, 4])}G"
preemptible: 2
}
output {
File out = select_first([outputFilename, "generated"])
File out_tbi = select_first([outputFilename, "generated"]) + ".tbi"
}
}
Common Workflow Language¶
#!/usr/bin/env cwl-runner
class: CommandLineTool
cwlVersion: v1.2
label: 'GATK4: SelectVariants'
doc: |
USAGE: Selectvariants [arguments]
This tool makes it possible to select a subset of variants based on various criteria in order to facilitate certain
analyses. Examples include comparing and contrasting cases vs. controls, extracting variant or non-variant loci that
meet certain requirements, or troubleshooting some unexpected results, to name a few.
Version:4.1.3.0
requirements:
- class: ShellCommandRequirement
- class: InlineJavascriptRequirement
- class: DockerRequirement
dockerPull: broadinstitute/gatk:4.1.4.0
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: outputFilename
label: outputFilename
doc: (--output) Required.
type:
- string
- 'null'
default: generated
inputBinding:
prefix: -O
separate: true
- id: variants
label: variants
doc: (--variant) A VCF file containing variants Required.
type:
- File
- 'null'
secondaryFiles:
- pattern: .tbi
inputBinding:
prefix: -V
separate: true
- 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:Boolean
separate: true
- 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
separate: true
- 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
separate: true
- id: cloudIndexPrefetchBuffer
label: cloudIndexPrefetchBuffer
doc: |-
(-CIPB:Integer) 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
separate: true
- id: cloudPrefetchBuffer
label: cloudPrefetchBuffer
doc: |-
(-CPB:Integer) Size of the cloud-only prefetch buffer (in MB; 0 to disable). Default value: 40.
type:
- int
- 'null'
inputBinding:
prefix: --cloud-prefetch-buffer
separate: true
- id: conc
label: conc
doc: |-
(--concordance) Output variants also called in this comparison track Default value: null.
type:
- string
- 'null'
inputBinding:
prefix: -conc
separate: true
- 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
default: true
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:Boolean) 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: {WellformedReadFilter}
type:
- string
- 'null'
inputBinding:
prefix: --disable-read-filter
separate: true
- 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: disc
label: disc
doc: |-
(--discordance) Output variants not called in this comparison track Default value: null.
type:
- string
- 'null'
inputBinding:
prefix: -disc
separate: true
- id: dropGenotypeAnnotation
label: dropGenotypeAnnotation
doc: |-
(-DGA:String) Genotype annotations to drop from output vcf. Annotations to be dropped are specified by their key. This argument may be specified 0 or more times. Default value: null.
type:
- string
- 'null'
inputBinding:
prefix: --drop-genotype-annotation
separate: true
- id: dropInfoAnnotation
label: dropInfoAnnotation
doc: |-
(-DA:String) Info annotations to drop from output vcf. Annotations to be dropped are specified by their key. This argument may be specified 0 or more times. Default value: null.
type:
- string
- 'null'
inputBinding:
prefix: --drop-info-annotation
separate: true
- id: excludeFiltered
label: excludeFiltered
doc: |-
Don't include filtered sites Default value: false. Possible values: {true, false}
type:
- boolean
- 'null'
inputBinding:
prefix: --exclude-filtered
- id: xlIds
label: xlIds
doc: |-
(--exclude-ids) List of variant rsIDs to exclude This argument may be specified 0 or more times. Default value: null.
type:
- string
- 'null'
inputBinding:
prefix: -xl-ids
separate: true
- id: excludeIntervals
label: excludeIntervals
doc: '(-XL) This argument may be specified 0 or more times. Default value: null. '
type:
- string
- 'null'
inputBinding:
prefix: --exclude-intervals
separate: true
- id: excludeNonvariants
label: excludeNonvariants
doc: 'Default value: false. Possible values: {true, false}'
type:
- string
- 'null'
inputBinding:
prefix: --exclude-non-variants
- id: excludeSampleExpressions
label: excludeSampleExpressions
doc: |-
(-xl-se:String) List of sample expressions to exclude This argument may be specified 0 or more times. Default value: null.
type:
- string
- 'null'
inputBinding:
prefix: --exclude-sample-expressions
separate: true
- id: excludeSampleName
label: excludeSampleName
doc: |-
(-xl-sn:String) Exclude genotypes from this sample This argument may be specified 0 or more times. Default value: null.
type:
- string
- 'null'
inputBinding:
prefix: --exclude-sample-name
separate: true
- id: gatkConfigFile
label: gatkConfigFile
doc: 'A configuration file to use with the GATK. Default value: null.'
type:
- File
- 'null'
inputBinding:
prefix: --gatk-config-file
separate: true
- 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
separate: true
- 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
separate: true
- id: help
label: help
doc: |-
(--help) display the help message Default value: false. Possible values: {true, false}
type:
- boolean
- 'null'
inputBinding:
prefix: -h
- id: bam
label: bam
doc: |-
(--input) BAM/SAM/CRAM file containing reads This argument may be specified 0 or more times. Default value: null.
type:
- File
- 'null'
secondaryFiles:
- pattern: .bai
inputBinding:
prefix: -I
separate: true
- id: intervalExclusionPadding
label: intervalExclusionPadding
doc: |-
(-ixp:Integer) Amount of padding (in bp) to add to each interval you are excluding. Default value: 0.
type:
- int
- 'null'
inputBinding:
prefix: --interval-exclusion-padding
separate: true
- 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: -imr
separate: true
- id: ip
label: ip
doc: '(--interval-padding) Default value: 0.'
type:
- int
- 'null'
inputBinding:
prefix: -ip
separate: true
- 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: -isr
separate: true
- id: intervals
label: intervals
doc: |-
(-L:String) One or more genomic intervals over which to operate This argument may be specified 0 or more times. Default value: null.
type:
- string
- 'null'
inputBinding:
prefix: --intervals
separate: true
- id: invertMendelianViolation
label: invertMendelianViolation
doc: |2-
Output non-mendelian violation sites only Default value: false. Possible values: {true, false}
type:
- boolean
- 'null'
inputBinding:
prefix: --invert-mendelian-violation
- id: invertSelect
label: invertSelect
doc: |-
(--invertSelect) Invert the selection criteria for -select Default value: false. Possible values: {true, false}
type:
- boolean
- 'null'
inputBinding:
prefix: -invert-select
- id: ids
label: ids
doc: |-
(--keep-ids) List of variant rsIDs to select This argument may be specified 0 or more times. Default value: null.
type:
- string
- 'null'
inputBinding:
prefix: -ids
separate: true
- id: keepOriginalAc
label: keepOriginalAc
doc: |-
Store the original AC, AF, and AN values after subsetting Default value: false. Possible values: {true, false}
type:
- boolean
- 'null'
inputBinding:
prefix: --keep-original-ac
- id: keepOriginalDp
label: keepOriginalDp
doc: |-
Store the original DP value after subsetting Default value: false. Possible values: {true, false}
type:
- boolean
- 'null'
inputBinding:
prefix: --keep-original-dp
separate: true
- id: le
label: le
doc: |-
(--lenient) Lenient processing of VCF files Default value: false. Possible values: {true, false}
type:
- boolean
- 'null'
inputBinding:
prefix: -LE
separate: true
- id: maxFilteredGenotypes
label: maxFilteredGenotypes
doc: |-
Maximum number of samples filtered at the genotype level Default value: 2147483647.
type:
- int
- 'null'
inputBinding:
prefix: --max-filtered-genotypes
separate: true
- id: maxFractionFilteredGenotypes
label: maxFractionFilteredGenotypes
doc: |2-
Maximum fraction of samples filtered at the genotype level Default value: 1.0.
type:
- double
- 'null'
inputBinding:
prefix: --max-fraction-filtered-genotypes
separate: true
- id: maxIndelSize
label: maxIndelSize
doc: 'Maximum size of indels to include Default value: 2147483647.'
type:
- int
- 'null'
inputBinding:
prefix: --max-indel-size
separate: true
- id: maxNocallFraction
label: maxNocallFraction
doc: 'Maximum fraction of samples with no-call genotypes Default value: 1.0.'
type:
- double
- 'null'
inputBinding:
prefix: --max-nocall-fraction
separate: true
- id: maxNocallNumber
label: maxNocallNumber
doc: 'Maximum number of samples with no-call genotypes Default value: 2147483647.'
type:
- int
- 'null'
inputBinding:
prefix: --max-nocall-number
separate: true
- id: mendelianViolation
label: mendelianViolation
doc: 'Default value: false. Possible values: {true, false} '
type:
- boolean
- 'null'
inputBinding:
prefix: --mendelian-violation
separate: true
- id: mendelianViolationQualThreshold
label: mendelianViolationQualThreshold
doc: |2-
Minimum GQ score for each trio member to accept a site as a violation Default value: 0.0.
type:
- double
- 'null'
inputBinding:
prefix: --mendelian-violation-qual-threshold
separate: true
- id: minFilteredGenotypes
label: minFilteredGenotypes
doc: ' Minimum number of samples filtered at the genotype level Default value:
0. '
type:
- int
- 'null'
inputBinding:
prefix: --min-filtered-genotypes
separate: true
- id: minFractionFilteredGenotypes
label: minFractionFilteredGenotypes
doc: |2-
Maximum fraction of samples filtered at the genotype level Default value: 0.0.
type:
- double
- 'null'
inputBinding:
prefix: --min-fraction-filtered-genotypes
separate: true
- id: minIndelSize
label: minIndelSize
doc: 'Minimum size of indels to include Default value: 0.'
type:
- int
- 'null'
inputBinding:
prefix: --min-indel-size
separate: true
- id: pedigree
label: pedigree
doc: '(-ped:File) Pedigree file Default value: null.'
type:
- File
- 'null'
inputBinding:
prefix: --pedigree
separate: true
- id: preserveAlleles
label: preserveAlleles
doc: |-
Preserve original alleles, do not trim Default value: false. Possible values: {true, false}
type:
- boolean
- 'null'
inputBinding:
prefix: --preserve-alleles
separate: true
- 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
separate: true
- id: readFilter
label: readFilter
doc: |-
(-RF:String) 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, SoftClippedReadFilter, ValidAlignmentEndReadFilter, ValidAlignmentStartReadFilter, WellformedReadFilter}
type:
- string
- 'null'
inputBinding:
prefix: --read-filter
separate: true
- 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:
- File
- 'null'
inputBinding:
prefix: -read-index
separate: true
- 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
separate: true
- id: reference
label: reference
doc: '(-R:String) Reference sequence Default value: null.'
type:
- File
- 'null'
secondaryFiles:
- pattern: .fai
- pattern: .amb
- pattern: .ann
- pattern: .bwt
- pattern: .pac
- pattern: .sa
- pattern: ^.dict
inputBinding:
prefix: --reference
separate: true
- id: removeFractionGenotypes
label: removeFractionGenotypes
doc: |2-
Select a fraction of genotypes at random from the input and sets them to no-call Default value: 0.0.
type:
- double
- 'null'
inputBinding:
prefix: --remove-fraction-genotypes
separate: true
- id: removeUnusedAlternates
label: removeUnusedAlternates
doc: |2-
Remove alternate alleles not present in any genotypes Default value: false. Possible values: {true, false}
type:
- boolean
- 'null'
inputBinding:
prefix: --remove-unused-alternates
separate: true
- id: restrictAllelesTo
label: restrictAllelesTo
doc: |2-
Select only variants of a particular allelicity Default value: ALL. Possible values: {ALL, BIALLELIC, MULTIALLELIC}
type:
- string
- 'null'
inputBinding:
prefix: --restrict-alleles-to
separate: true
- id: sampleExpressions
label: sampleExpressions
doc: |-
(-se:String) Regular expression to select multiple samples This argument may be specified 0 or more times. Default value: null.
type:
- string
- 'null'
inputBinding:
prefix: --sample-expressions
separate: true
- id: sampleName
label: sampleName
doc: |-
(-sn:String) Include genotypes from this sample This argument may be specified 0 or more times. Default value: null.
type:
- string
- 'null'
inputBinding:
prefix: --sample-name
separate: true
- 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
separate: true
- id: selectRandomFraction
label: selectRandomFraction
doc: |-
(-fraction:Double) Select a fraction of variants at random from the input Default value: 0.0.
type:
- string
- 'null'
inputBinding:
prefix: --select-random-fraction
separate: true
- id: selectTypeToExclude
label: selectTypeToExclude
doc: |-
(-xl-select-type:Type) Do not select certain type of variants from the input file This argument may be specified 0 or more times. Default value: null. Possible values: {NO_VARIATION, SNP, MNP, INDEL, SYMBOLIC, MIXED}
type:
- string
- 'null'
inputBinding:
prefix: --select-type-to-exclude
separate: true
- id: selectTypeToInclude
label: selectTypeToInclude
doc: |-
(-select-type:Type) Select only a certain type of variants from the input file This argument may be specified 0 or more times. Default value: null. Possible values: {NO_VARIATION, SNP, MNP, INDEL, SYMBOLIC, MIXED}
type:
- string
- 'null'
inputBinding:
prefix: --select-type-to-include
separate: true
- id: selectexpressions
label: selectexpressions
doc: |-
(-select:String) One or more criteria to use when selecting the data This argument may be specified 0 or more times. Default value: null.
type:
- string
- 'null'
inputBinding:
prefix: --selectExpressions
separate: true
- 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:
- File
- 'null'
inputBinding:
prefix: -sequence-dictionary
separate: true
- id: setFilteredGtToNocall
label: setFilteredGtToNocall
doc: |2-
Set filtered genotypes to no-call Default value: false. Possible values: {true, false}
type:
- boolean
- 'null'
inputBinding:
prefix: --set-filtered-gt-to-nocall
separate: true
- 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
separate: true
- id: tmpDir
label: tmpDir
doc: 'Temp directory to use. Default value: null.'
type:
- string
- 'null'
default: generated
inputBinding:
prefix: --tmp-dir
separate: true
- 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
separate: true
- 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
separate: true
- 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
separate: true
- 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
separate: true
- 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
separate: true
- id: showhidden
label: showhidden
doc: |-
(--showHidden) display hidden arguments Default value: false. Possible values: {true, false}
type:
- boolean
- 'null'
inputBinding:
prefix: -showHidden
separate: true
- id: ambigFilterBases
label: ambigFilterBases
doc: |-
Valid only if 'AmbiguousBaseReadFilter' is specified: 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
separate: true
- id: ambigFilterFrac
label: ambigFilterFrac
doc: |-
Valid only if 'AmbiguousBaseReadFilter' is specified: 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
separate: true
- id: maxFragmentLength
label: maxFragmentLength
doc: |-
Valid only if 'FragmentLengthReadFilter' is specified: Maximum length of fragment (insert size) Default value: 1000000.
type:
- int
- 'null'
inputBinding:
prefix: --max-fragment-length
separate: true
- id: minFragmentLength
label: minFragmentLength
doc: |-
Valid only if 'FragmentLengthReadFilter' is specified: Minimum length of fragment (insert size) Default value: 0.
type:
- int
- 'null'
inputBinding:
prefix: --min-fragment-length
separate: true
- id: keepIntervals
label: keepIntervals
doc: |-
Valid only if 'IntervalOverlapReadFilter' is specified: One or more genomic intervals to keep This argument must be specified at least once. Required.
type:
- string
- 'null'
inputBinding:
prefix: --keep-intervals
separate: true
- id: library
label: library
doc: |-
Valid only if 'LibraryReadFilter' is specified: (--library) Name of the library to keep This argument must be specified at least once. Required.
type:
- string
- 'null'
inputBinding:
prefix: -library
separate: true
- id: maximumMappingQuality
label: maximumMappingQuality
doc: |-
Valid only if 'MappingQualityReadFilter' is specified: Maximum mapping quality to keep (inclusive) Default value: null.
type:
- int
- 'null'
inputBinding:
prefix: --maximum-mapping-quality
separate: true
- id: minimumMappingQuality
label: minimumMappingQuality
doc: |-
Valid only if 'MappingQualityReadFilter' is specified: Minimum mapping quality to keep (inclusive) Default value: 10.
type:
- int
- 'null'
inputBinding:
prefix: --minimum-mapping-quality
separate: true
- id: dontRequireSoftClipsBothEnds
label: dontRequireSoftClipsBothEnds
doc: |-
Valid only if 'OverclippedReadFilter' is specified: 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
separate: true
- id: filterTooShort
label: filterTooShort
doc: |-
Valid only if 'OverclippedReadFilter' is specified: Minimum number of aligned bases Default value: 30.
type:
- int
- 'null'
inputBinding:
prefix: --filter-too-short
separate: true
- id: platformFilterName
label: platformFilterName
doc: |-
Valid only if 'PlatformReadFilter' is specified: This argument must be specified at least once. Required.
type:
- string
- 'null'
inputBinding:
prefix: --platform-filter-name
separate: true
- id: blackListedLanes
label: blackListedLanes
doc: |-
Valid only if 'PlatformUnitReadFilter' is specified: Platform unit (PU) to filter out This argument must be specified at least once. Required.
type:
- string
- 'null'
inputBinding:
prefix: --black-listed-lanes
separate: true
- id: readGroupBlackList
label: readGroupBlackList
doc: |-
Valid only if 'ReadGroupBlackListReadFilter' is specified: The name of the read group to filter out. This argument must be specified at least once. Required.
type:
- string
- 'null'
inputBinding:
prefix: --read-group-black-list
separate: true
- id: keepReadGroup
label: keepReadGroup
doc: |-
Valid only if 'ReadGroupReadFilter' is specified: The name of the read group to keep Required.
type:
- string
- 'null'
inputBinding:
prefix: --keep-read-group
separate: true
- id: maxReadLength
label: maxReadLength
doc: |-
Valid only if 'ReadLengthReadFilter' is specified: Keep only reads with length at most equal to the specified value Required.
type:
- int
- 'null'
inputBinding:
prefix: --max-read-length
separate: true
- id: minReadLength
label: minReadLength
doc: |-
Valid only if 'ReadLengthReadFilter' is specified: Keep only reads with length at least equal to the specified value Default value: 1.
type:
- int
- 'null'
inputBinding:
prefix: --min-read-length
separate: true
- id: readName
label: readName
doc: |-
Valid only if 'ReadNameReadFilter' is specified: Keep only reads with this read name Required.
type:
- string
- 'null'
inputBinding:
prefix: --read-name
separate: true
- id: keepReverseStrandOnly
label: keepReverseStrandOnly
doc: |-
Valid only if 'ReadStrandFilter' is specified: Keep only reads on the reverse strand Required. Possible values: {true, false}
type:
- boolean
- 'null'
inputBinding:
prefix: --keep-reverse-strand-only
separate: true
- id: sample
label: sample
doc: |-
Valid only if 'SampleReadFilter' is specified: 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
separate: true
- id: invertSoftClipRatioFilter
label: invertSoftClipRatioFilter
doc: |2-
Inverts the results from this filter, causing all variants that would pass to fail and visa-versa. Default value: false. Possible values: {true, false}
type:
- boolean
- 'null'
inputBinding:
prefix: --invert-soft-clip-ratio-filter
separate: true
- id: softClippedLeadingTrailingRatio
label: softClippedLeadingTrailingRatio
doc: |2-
Threshold ratio of soft clipped bases (leading / trailing the cigar string) to total bases in read for read to be filtered. Default value: null. Cannot be used in conjuction with argument(s) minimumSoftClippedRatio
type:
- double
- 'null'
inputBinding:
prefix: --soft-clipped-leading-trailing-ratio
separate: true
- id: softClippedRatioThreshold
label: softClippedRatioThreshold
doc: |2-
Threshold ratio of soft clipped bases (anywhere in the cigar string) to total bases in read for read to be filtered. Default value: null. Cannot be used in conjuction with argument(s) minimumLeadingTrailingSoftClippedRatio
type:
- double
- 'null'
inputBinding:
prefix: --soft-clipped-ratio-threshold
separate: true
outputs:
- id: out
label: out
type: File
secondaryFiles:
- pattern: .tbi
outputBinding:
glob: generated
loadContents: false
stdout: _stdout
stderr: _stderr
baseCommand:
- gatk
- SelectVariants
arguments:
- prefix: --java-options
position: -1
valueFrom: |-
$("-Xmx{memory}G {compression} {otherargs}".replace(/\{memory\}/g, (([inputs.runtime_memory, 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: Gatk4SelectVariants