HaplotypeCaller and Read Group Errors
GATK version used: 4.1.9.0
(1) trying to use HaplotypeCaller including "--java-options "Xmx4g" command.
Exact command used:
(base) Juliannes-MacBook-Pro:gatk-4.1.9.0 julianneradford$ ./gatk --java-options "-Xmx4g" --java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true' HaplotypeCaller \
> -R Rflav_transcriptome_sequences.fa \
> -I SRR5341585.bam \
> -O 85variants.g.vcf \
> -ERC GVCF \
> --Galaxy54-[MarkDuplicates_on_data_138__MarkDuplicates_BAM_output]
c) Entire error log:
Using GATK jar /Applications/CompSci/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx4g -jar /Applications/CompSci/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar --java-options -DGATK_STACKTRACE_ON_USER_EXCEPTION=true HaplotypeCaller -R Rflav_transcriptome_sequences.fa -I SRR5341585.bam -O 85variants.g.vcf -ERC GVCF --Galaxy54-[MarkDuplicates_on_data_138__MarkDuplicates_BAM_output]
USAGE: <program name> [-h]
Available Programs:...
A USER ERROR has occurred: '--java-options' is not a valid command.=
(2) Running HaplotypeCaller without the --java-options command
Entire command:
(base) Juliannes-MacBook-Pro:gatk-4.1.9.0 julianneradford$ ./gatk --java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true' HaplotypeCaller \
> -R Rflav_transcriptome_sequences.fa \
> -I SRR5341585.bam \
> -O 85variants.g.vcf \
> -ERC GVCF \
> --Galaxy54-[MarkDuplicates_on_data_138__MarkDuplicates_BAM_output]
Entire error log:
Using GATK jar /Applications/CompSci/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -DGATK_STACKTRACE_ON_USER_EXCEPTION=true -jar /Applications/CompSci/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar HaplotypeCaller -R Rflav_transcriptome_sequences.fa -I SRR5341585.bam -O 85variants.g.vcf -ERC GVCF --Galaxy54-[MarkDuplicates_on_data_138__MarkDuplicates_BAM_output]
USAGE: HaplotypeCaller [arguments]
Call germline SNPs and indels via local re-assembly of haplotypes
Version:4.1.9.0
Required Arguments:
--input,-I <GATKPath> BAM/SAM/CRAM file containing reads This argument must be specified at least once.
Required.
--output,-O <String> File to which variants should be written Required.
--reference,-R <GATKPath> Reference sequence file 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}
--alleles <FeatureInput> The set of alleles to force-call regardless of evidence Default value: null.
--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: {AlleleFraction,
AS_BaseQualityRankSumTest, AS_FisherStrand, AS_InbreedingCoeff,
AS_MappingQualityRankSumTest, AS_QualByDepth, AS_ReadPosRankSumTest, AS_RMSMappingQuality,
AS_StrandBiasMutectAnnotation, AS_StrandOddsRatio, BaseQuality, BaseQualityHistogram,
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, UniqueAltReadCountPossible values: {
--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:
{AlleleSpecificAnnotation, AS_StandardAnnotation, ReducibleAnnotation, StandardAnnotation,
StandardHCAnnotation, StandardMutectAnnotationPossible values: {
--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, DepthPerSampleHC, ExcessHet,
FisherStrand, InbreedingCoeff, MappingQualityRankSumTest, QualByDepth, ReadPosRankSumTest,
RMSMappingQuality, StrandOddsRatioPossible values: {
--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.
--assembly-region-out <String>Output the assembly region to this IGV formatted file Default value: null.
--assembly-region-padding <Integer>
Number of additional bases of context to include around each assembly region Default
value: 100.
--base-quality-score-threshold <Byte>
Base qualities below this threshold will be reduced to the minimum (6) Default value: 18.
--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.
--contamination-fraction-to-filter,-contamination <Double>
Fraction of contamination in sequencing data (for all samples) to aggressively remove
Default value: 0.0.
--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: {GoodCigarReadFilter, MappedReadFilter,
MappingQualityAvailableReadFilter, MappingQualityReadFilter,
NonZeroReferenceLengthAlignmentReadFilter, NotDuplicateReadFilter,
NotSecondaryAlignmentReadFilter, PassesVendorQualityCheckReadFilter,
WellformedReadFilterPossible values: {
--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 <String>
One 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.
--gcs-project-for-requester-pays <String>
Project to bill when accessing "requester pays" buckets. If unset, these buckets cannot be
accessed. User must have storage.buckets.get permission on the bucket being accessed.
Default value: .
--graph-output,-graph <String>Write debug assembly graph information to this file Default value: null.
--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.
--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 <Integer>
Amount 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}
--max-assembly-region-size <Integer>
Maximum size of an assembly region Default value: 300.
--max-reads-per-alignment-start <Integer>
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.
--min-assembly-region-size <Integer>
Minimum size of an assembly region Default value: 50.
--min-base-quality-score,-mbq <Byte>
Minimum base quality required to consider a base for calling Default value: 10.
--native-pair-hmm-threads <Integer>
How many threads should a native pairHMM implementation use Default value: 4.
--native-pair-hmm-use-double-precision <Boolean>
use double precision in the native pairHmm. This is slower but matches the java
implementation better 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.
--output-mode <OutputMode> Specifies which type of calls we should output Default value: EMIT_VARIANTS_ONLY.
Possible values: {EMIT_VARIANTS_ONLY, EMIT_ALL_CONFIDENT_SITES, EMIT_ALL_ACTIVE_SITES}
--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, IntervalOverlapReadFilter, LibraryReadFilter, MappedReadFilter,
MappingQualityAvailableReadFilter, MappingQualityNotZeroReadFilter,
MappingQualityReadFilter, MatchingBasesAndQualsReadFilter, MateDifferentStrandReadFilter,
MateDistantReadFilter, MateOnSameContigOrNoMappedMateReadFilter,
MateUnmappedAndUnmappedReadFilter, MetricsReadFilter,
NonChimericOriginalAlignmentReadFilter, NonZeroFragmentLengthReadFilter,
NonZeroReferenceLengthAlignmentReadFilter, NotDuplicateReadFilter,
NotOpticalDuplicateReadFilter, NotProperlyPairedReadFilter,
NotSecondaryAlignmentReadFilter, NotSupplementaryAlignmentReadFilter,
OverclippedReadFilter, PairedReadFilter, PassesVendorQualityCheckReadFilter,
PlatformReadFilter, PlatformUnitReadFilter, PrimaryLineReadFilter,
ProperlyPairedReadFilter, ReadGroupBlackListReadFilter, ReadGroupReadFilter,
ReadLengthEqualsCigarLengthReadFilter, ReadLengthReadFilter, ReadNameReadFilter,
ReadStrandFilter, SampleReadFilter, SecondOfPairReadFilter, SeqIsStoredReadFilter,
SoftClippedReadFilter, ValidAlignmentEndReadFilter, ValidAlignmentStartReadFilter,
WellformedReadFilterPossible values: {
--read-index,-read-index <GATKPath>
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}
--recover-dangling-heads <Boolean>
This argument is deprecated since version 3.3 Default value: false. Possible values:
{true, false}
--sample-name,-ALIAS <String> Name of single sample to use from a multi-sample bam Default value: null.
--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: 30.0.
--tmp-dir <GATKPath> Temp directory to use. 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}
--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:
--active-probability-threshold <Double>
Minimum probability for a locus to be considered active. Default value: 0.002.
--adaptive-pruning <Boolean> Use Mutect2's adaptive graph pruning algorithm Default value: false. Possible values:
{true, false}
--adaptive-pruning-initial-error-rate <Double>
Initial base error rate estimate for adaptive pruning Default value: 0.001.
--all-site-pls <Boolean> Annotate all sites with PLs Default value: false. Possible values: {true, false}
--allele-informative-reads-overlap-margin <Integer>
Likelihood and read-based annotations will only take into consideration reads that overlap
the variant or any base no further than this distance expressed in base pairs Default
value: 2.
--allow-non-unique-kmers-in-ref <Boolean>
Allow graphs that have non-unique kmers in the reference Default value: false. Possible
values: {true, false}
--bam-output,-bamout <String> File to which assembled haplotypes should be written Default value: null.
--bam-writer-type <WriterType>Which haplotypes should be written to the BAM Default value: CALLED_HAPLOTYPES. Possible
values: {ALL_POSSIBLE_HAPLOTYPES, CALLED_HAPLOTYPES}
--comparison,-comp <FeatureInput>
Comparison VCF file(s) This argument may be specified 0 or more times. Default value:
null.
--contamination-fraction-per-sample-file,-contamination-file <File>
Tab-separated File containing fraction of contamination in sequencing data (per sample) to
aggressively remove. Format should be "<SampleID><TAB><Contamination>" (Contamination is
double) per line; No header. Default value: null.
--debug-assembly,-debug <Boolean>
Print out verbose debug information about each assembly region Default value: false.
Possible values: {true, false}
--disable-optimizations <Boolean>
Don't skip calculations in ActiveRegions with no variants Default value: false. Possible
values: {true, false}
--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}
--do-not-correct-overlapping-quality <Boolean>
Disable overlapping base quality correction Default value: false. Possible values: {true,
false}
--do-not-run-physical-phasing <Boolean>
Disable physical phasing Default value: false. Possible values: {true, false}
--dont-increase-kmer-sizes-for-cycles <Boolean>
Disable iterating over kmer sizes when graph cycles are detected Default value: false.
Possible values: {true, false}
--dont-use-soft-clipped-bases <Boolean>
Do not analyze soft clipped bases in the reads Default value: false. Possible values:
{true, false}
--emit-ref-confidence,-ERC <ReferenceConfidenceMode>
Mode for emitting reference confidence scores (For Mutect2, this is a BETA feature)
Default value: NONE. Possible values: {NONE, BP_RESOLUTION, GVCF}
--enable-all-annotations <Boolean>
Use all possible annotations (not for the faint of heart) Default value: false. Possible
values: {true, false}
--floor-blocks <Boolean> Output the band lower bound for each GQ block regardless of the data it represents
Default value: false. Possible values: {true, false}
--force-active <Boolean> If provided, all regions will be marked as active Default value: false. Possible values:
{true, false}
--force-call-filtered-alleles,-genotype-filtered-alleles <Boolean>
Force-call filtered alleles included in the resource specified by --alleles Default
value: false. Possible values: {true, false}
--gvcf-gq-bands,-GQB <Integer>Exclusive upper bounds for reference confidence GQ bands (must be in [1, 100] and
specified in increasing order) This argument may be specified 0 or more times. Default
value: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23,
24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45,
46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 70, 80, 90, 99].
--indel-size-to-eliminate-in-ref-model <Integer>
The size of an indel to check for in the reference model Default value: 10.
--kmer-size <Integer> Kmer size to use in the read threading assembler This argument may be specified 0 or more
times. Default value: [10, 25].
--linked-de-bruijn-graph <Boolean>
If enabled, the Assembly Engine will construct a Linked De Bruijn graph to recover better
haplotypes Default value: false. Possible values: {true, false}
--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.
--max-mnp-distance,-mnp-dist <Integer>
Two or more phased substitutions separated by this distance or less are merged into MNPs.
Default value: 0.
--max-num-haplotypes-in-population <Integer>
Maximum number of haplotypes to consider for your population Default value: 128.
--max-prob-propagation-distance <Integer>
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.
--max-unpruned-variants <Integer>
Maximum number of variants in graph the adaptive pruner will allow Default value: 100.
--min-dangling-branch-length <Integer>
Minimum length of a dangling branch to attempt recovery Default value: 4.
--min-pruning <Integer> Minimum support to not prune paths in the graph Default value: 2.
--num-pruning-samples <Integer>
Number of samples that must pass the minPruning threshold Default value: 1.
--pair-hmm-gap-continuation-penalty <Integer>
Flat gap continuation penalty for use in the Pair HMM Default value: 10.
--pair-hmm-implementation,-pairHMM <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}
--pcr-indel-model <PCRErrorModel>
The PCR indel model to use Default value: CONSERVATIVE. Possible values: {NONE, HOSTILE,
AGGRESSIVE, CONSERVATIVE}
--phred-scaled-global-read-mismapping-rate <Integer>
The global assumed mismapping rate for reads Default value: 45.
--pruning-lod-threshold <Double>
Ln likelihood ratio threshold for adaptive pruning algorithm Default value:
2.302585092994046.
--pruning-seeding-lod-threshold <Double>
Ln likelihood ratio threshold for seeding subgraph of good variation in adaptive pruning
algorithm Default value: 9.210340371976184.
--recover-all-dangling-branches <Boolean>
Recover all dangling branches Default value: false. Possible values: {true, false}
--showHidden,-showHidden <Boolean>
display hidden arguments Default value: false. Possible values: {true, false}
--smith-waterman <Implementation>
Which Smith-Waterman implementation to use, generally FASTEST_AVAILABLE is the right
choice Default value: JAVA. Possible values: {FASTEST_AVAILABLE, AVX_ENABLED, JAVA}
--use-filtered-reads-for-annotations <Boolean>
Use the contamination-filtered read maps for the purposes of annotating variants Default
value: false. Possible values: {true, false}
Conditional Arguments for annotation:
Valid only if "RMSMappingQuality" is specified:
--allow-old-rms-mapping-quality-annotation-data <Boolean>
Override to allow old RMSMappingQuality annotated VCFs to function Default value: false.
Possible values: {true, false}
Conditional Arguments for readFilter:
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 conjunction with
argument(s) maxAmbiguousBaseFraction
--ambig-filter-frac <Double> Threshold fraction of ambiguous bases Default value: 0.05. Cannot be used in conjunction
with argument(s) maxAmbiguousBases
Valid only if "FragmentLengthReadFilter" is specified:
--max-fragment-length <Integer>
Maximum length of fragment (insert size) Default value: 1000000.
--min-fragment-length <Integer>
Minimum length of fragment (insert size) Default value: 0.
Valid only if "IntervalOverlapReadFilter" is specified:
--keep-intervals <String> One or more genomic intervals to keep This argument must be specified at least once.
Required.
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: 20.
Valid only if "MateDistantReadFilter" is specified:
--mate-too-distant-length <Integer>
Minimum start location difference at which mapped mates are considered distant Default
value: 1000.
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 <String>
A read group filter expression in the form "attribute:value", where "attribute" is a two
character read group attribute such as "RG" or "PU". 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.
Valid only if "SoftClippedReadFilter" is specified:
--invert-soft-clip-ratio-filter <Boolean>
Inverts the results from this filter, causing all variants that would pass to fail and
visa-versa. Default value: false. Possible values: {true, false}
--soft-clipped-leading-trailing-ratio <Double>
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 conjunction with
argument(s) minimumSoftClippedRatio
--soft-clipped-ratio-threshold <Double>
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 conjunction with
argument(s) minimumLeadingTrailingSoftClippedRatio
***********************************************************************
A USER ERROR has occurred: Galaxy54-[MarkDuplicates_on_data_138__MarkDuplicates_BAM_output] is not a recognized option
***********************************************************************
org.broadinstitute.barclay.argparser.CommandLineException: Galaxy54-[MarkDuplicates_on_data_138__MarkDuplicates_BAM_output] is not a recognized option
at org.broadinstitute.barclay.argparser.CommandLineArgumentParser.parseArguments(CommandLineArgumentParser.java:149)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.parseArgs(CommandLineProgram.java:233)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:207)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)
at org.broadinstitute.hellbender.Main.main(Main.java:289)
So the new error is the sample name input for the BAM file. For this, I used the name of the BAM file when I downloaded it from Galaxy, because this is supposed to be the sample name (and there is only one paired sample per bam file). However, I went to the Read Group documentation page, and used the following command to try and get the sample name from the bam file:
view -H SRR5341585.bam | grep '@RG'
and retrieved the error:
E26: Hebrew cannot be used: Not enabled at compile time
So that is where I am at with my HaplotypeCaller journey, I really appreciate all of your help or any suggestions you may have!
PS.
Unrelated to the above issue:
Why do I have to re-add samtools and gatk to the $PATH every time I open a new shell? Is there a way to add them permanently? And the commands will not work unless they are added to the path and I cd to the directory that they are in. If I want to use a samtools tool, I have to cd to samtools, then when I want to use gatk, I have to cd back to gatk. Is this normal?
Thanks again,
Julie
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Hi Julianne Radford,
Please see this document for command line usage recommendations, including how to use java options: https://gatk.broadinstitute.org/hc/en-us/articles/360035531892-GATK4-command-line-syntax
Regarding your path, there may be more information on that in other bioinformatics blogs, our first priority is GATK issues, but we will add this question to our backlog if time allows.
Best,
Genevieve
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