Hi! I've looked through the forums and help, but I can't find an option that does what I want it to do.
When I'm debugging a pipeline, whenever an error occurs, the tool that receives the error prints out the man page to my terminal prior to printing out the suspected cause of the error.
Is there an option to suppress outputting the man page? I'm using gatk v4.0.5.1
Here is an example:
command:
gatk GenotypeGVCFs -R /path/to/ref/GRCh38_.fa -V gendb://wild_dir -G StandardAnnotation -newQual -O wild_genotype.vcf
Output:
Perform joint genotyping on a single-sample GVCF from HaplotypeCaller or a multi-sample GVCF from CombineGVCFs or
GenomicsDBImport
Version:4.0.5.1
Required Arguments:
--output,-O:File File to which variants should be written Required.
--reference,-R:String Reference sequence file Required.
--variant,-V:String A VCF file containing variants Required.
Optional Arguments:
--add-output-sam-program-record,-add-output-sam-program-record:Boolean
If true, adds a PG tag to created SAM/BAM/CRAM files. Default value: true. Possible
values: {true, false}
--add-output-vcf-command-line,-add-output-vcf-command-line:Boolean
If true, adds a command line header line to created VCF files. Default value: true.
Possible values: {true, false}
--annotate-with-num-discovered-alleles:Boolean
If provided, we will annotate records with the number of alternate alleles that were
discovered (but not necessarily genotyped) at a given site Default value: false. Possible
values: {true, false}
--annotation,-A:String One or more specific annotations to add to variant calls This argument may be specified 0
or more times. Default value: null. Possible Values: {AS_BaseQualityRankSumTest,
AS_FisherStrand, AS_InbreedingCoeff, AS_MappingQualityRankSumTest, AS_QualByDepth,
AS_ReadPosRankSumTest, AS_RMSMappingQuality, AS_StrandOddsRatio, BaseQuality,
BaseQualityRankSumTest, ChromosomeCounts, ClippingRankSumTest, Coverage,
DepthPerAlleleBySample, DepthPerSampleHC, ExcessHet, FisherStrand, FragmentLength,
GenotypeSummaries, InbreedingCoeff, LikelihoodRankSumTest, MappingQuality,
MappingQualityRankSumTest, MappingQualityZero, OxoGReadCounts, PossibleDeNovo,
QualByDepth, ReadPosition, ReadPosRankSumTest, ReferenceBases, RMSMappingQuality,
SampleList, StrandArtifact, StrandBiasBySample, StrandOddsRatio, TandemRepeat,
UniqueAltReadCount}
--annotation-group,-G:String 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}
--annotations-to-exclude,-AX:String
One or more specific annotations to exclude from variant calls This argument may be
specified 0 or more times. Default value: null. Possible Values: {BaseQualityRankSumTest,
ChromosomeCounts, Coverage, DepthPerAlleleBySample, ExcessHet, FisherStrand,
InbreedingCoeff, MappingQualityRankSumTest, QualByDepth, ReadPosRankSumTest,
RMSMappingQuality, StrandOddsRatio}
--arguments_file: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.
--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.
--cloud-prefetch-buffer,-CPB:Integer
Size of the cloud-only prefetch buffer (in MB; 0 to disable). Default value: 40.
--create-output-bam-index,-OBI:Boolean
If true, create a BAM/CRAM index when writing a coordinate-sorted BAM/CRAM file. Default
value: true. Possible values: {true, false}
--create-output-bam-md5,-OBM:Boolean
If true, create a MD5 digest for any BAM/SAM/CRAM file created Default value: false.
Possible values: {true, false}
--create-output-variant-index,-OVI:Boolean
If true, create a VCF index when writing a coordinate-sorted VCF file. Default value:
true. Possible values: {true, false}
--create-output-variant-md5,-OVM:Boolean
If true, create a a MD5 digest any VCF file created. Default value: false. Possible
values: {true, false}
--dbsnp,-D:FeatureInput dbSNP file Default value: null.
--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}
--disable-read-filter,-DF:String
Read filters to be disabled before analysis This argument may be specified 0 or more
times. Default value: null. Possible Values: {WellformedReadFilter}
--disable-sequence-dictionary-validation,-disable-sequence-dictionary-validation:Boolean
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}
--exclude-intervals,-XL:StringOne or more genomic intervals to exclude from processing This argument may be specified 0
or more times. Default value: null.
--founder-id,-founder-id:String
Samples representing the population "founders" This argument may be specified 0 or more
times. Default value: null.
--gatk-config-file:String A configuration file to use with the GATK. Default value: null.
--gcs-max-retries,-gcs-retries:Integer
If the GCS bucket channel errors out, how many times it will attempt to re-initiate the
connection Default value: 20.
--help,-h:Boolean display the help message Default value: false. Possible values: {true, false}
--heterozygosity:Double Heterozygosity value used to compute prior likelihoods for any locus. See the GATKDocs
for full details on the meaning of this population genetics concept Default value: 0.001.
--heterozygosity-stdev:Double Standard deviation of heterozygosity for SNP and indel calling. Default value: 0.01.
--indel-heterozygosity:Double Heterozygosity for indel calling. See the GATKDocs for heterozygosity for full details on
the meaning of this population genetics concept Default value: 1.25E-4.
--input,-I:String BAM/SAM/CRAM file containing reads This argument may be specified 0 or more times.
Default value: null.
--interval-exclusion-padding,-ixp:Integer
Amount of padding (in bp) to add to each interval you are excluding. Default value: 0.
--interval-merging-rule,-imr:IntervalMergingRule
Interval merging rule for abutting intervals Default value: ALL. Possible values: {ALL,
OVERLAPPING_ONLY}
--interval-padding,-ip:IntegerAmount of padding (in bp) to add to each interval you are including. Default value: 0.
--interval-set-rule,-isr:IntervalSetRule
Set merging approach to use for combining interval inputs Default value: UNION. Possible
values: {UNION, INTERSECTION}
--intervals,-L:String One or more genomic intervals over which to operate This argument may be specified 0 or
more times. Default value: null.
--lenient,-LE:Boolean Lenient processing of VCF files Default value: false. Possible values: {true, false}
--num-reference-samples-if-no-call:Integer
Number of hom-ref genotypes to infer at sites not present in a panel Default value: 0.
--pedigree,-ped:File Pedigree file for determining the population "founders" Default value: null.
--population-callset,-population:FeatureInput
Callset to use in calculating genotype priors Default value: null.
--QUIET:Boolean Whether to suppress job-summary info on System.err. Default value: false. Possible
values: {true, false}
--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, LibraryReadFilter, MappedReadFilter,
MappingQualityAvailableReadFilter, MappingQualityNotZeroReadFilter,
MappingQualityReadFilter, MatchingBasesAndQualsReadFilter, MateDifferentStrandReadFilter,
MateOnSameContigOrNoMappedMateReadFilter, MetricsReadFilter,
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}
--read-index,-read-index:String
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.
--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}
--sample-ploidy,-ploidy:Integer
Ploidy (number of chromosomes) per sample. For pooled data, set to (Number of samples in
each pool * Sample Ploidy). Default value: 2.
--seconds-between-progress-updates,-seconds-between-progress-updates:Double
Output traversal statistics every time this many seconds elapse Default value: 10.0.
--sequence-dictionary,-sequence-dictionary:String
Use the given sequence dictionary as the master/canonical sequence dictionary. Must be a
.dict file. Default value: null.
--sites-only-vcf-output:Boolean
If true, don't emit genotype fields when writing vcf file output. Default value: false.
Possible values: {true, false}
--standard-min-confidence-threshold-for-calling,-stand-call-conf:Double
The minimum phred-scaled confidence threshold at which variants should be called Default
value: 10.0.
--TMP_DIR:File Undocumented option This argument may be specified 0 or more times. Default value: null.
--use-jdk-deflater,-jdk-deflater:Boolean
Whether to use the JdkDeflater (as opposed to IntelDeflater) Default value: false.
Possible values: {true, false}
--use-jdk-inflater,-jdk-inflater:Boolean
Whether to use the JdkInflater (as opposed to IntelInflater) Default value: false.
Possible values: {true, false}
--use-new-qual-calculator,-new-qual:Boolean
If provided, we will use the new AF model instead of the so-called exact model Default
value: false. Possible values: {true, false}
--verbosity,-verbosity:LogLevel
Control verbosity of logging. Default value: INFO. Possible values: {ERROR, WARNING,
INFO, DEBUG}
--version:Boolean display the version number for this tool Default value: false. Possible values: {true,
false}
Advanced Arguments:
--disable-tool-default-annotations,-disable-tool-default-annotations:Boolean
Disable all tool default annotations Default value: false. Possible values: {true, false}
--disable-tool-default-read-filters,-disable-tool-default-read-filters:Boolean
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}
--enable-all-annotations:Boolean
Use all possible annotations (not for the faint of heart) Default value: false. Possible
values: {true, false}
--input-prior:Double Input prior for calls This argument may be specified 0 or more times. Default value:
null.
--max-alternate-alleles:Integer
Maximum number of alternate alleles to genotype Default value: 6.
--max-genotype-count:Integer Maximum number of genotypes to consider at any site Default value: 1024.
--only-output-calls-starting-in-intervals:Boolean
Restrict variant output to sites that start within provided intervals Default value:
false. Possible values: {true, false}
--showHidden,-showHidden:Boolean
display hidden arguments Default value: false. Possible values: {true, false}
Conditional Arguments for read-filter:
Valid only if "AmbiguousBaseReadFilter" is specified:
--ambig-filter-bases:Integer 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
--ambig-filter-frac:Double Threshold fraction of ambiguous bases Default value: 0.05. Cannot be used in conjuction
with argument(s) maxAmbiguousBases
Valid only if "FragmentLengthReadFilter" is specified:
--max-fragment-length:Integer Maximum length of fragment (insert size) Default value: 1000000.
Valid only if "LibraryReadFilter" is specified:
--library,-library:String Name of the library to keep This argument must be specified at least once. Required.
Valid only if "MappingQualityReadFilter" is specified:
--maximum-mapping-quality:Integer
Maximum mapping quality to keep (inclusive) Default value: null.
--minimum-mapping-quality:Integer
Minimum mapping quality to keep (inclusive) Default value: 10.
Valid only if "OverclippedReadFilter" is specified:
--dont-require-soft-clips-both-ends:Boolean
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}
--filter-too-short:Integer Minimum number of aligned bases Default value: 30.
Valid only if "PlatformReadFilter" is specified:
--platform-filter-name:String Platform attribute (PL) to match This argument must be specified at least once. Required.
Valid only if "PlatformUnitReadFilter" is specified:
--black-listed-lanes:String Platform unit (PU) to filter out This argument must be specified at least once. Required.
Valid only if "ReadGroupBlackListReadFilter" is specified:
--read-group-black-list:StringThe name of the read group to filter out This argument must be specified at least once.
Required.
Valid only if "ReadGroupReadFilter" is specified:
--keep-read-group:String The name of the read group to keep Required.
Valid only if "ReadLengthReadFilter" is specified:
--max-read-length:Integer Keep only reads with length at most equal to the specified value Required.
--min-read-length:Integer Keep only reads with length at least equal to the specified value Default value: 1.
Valid only if "ReadNameReadFilter" is specified:
--read-name:String Keep only reads with this read name Required.
Valid only if "ReadStrandFilter" is specified:
--keep-reverse-strand-only:Boolean
Keep only reads on the reverse strand Required. Possible values: {true, false}
Valid only if "SampleReadFilter" is specified:
--sample,-sample:String The name of the sample(s) to keep, filtering out all others This argument must be
specified at least once. Required.
A USER ERROR has occurred: n is not a recognized option
I only want the last section where it tells me about the USER ERROR.
