Can you please provide
a) GATK version used : 4.1.6.0
Dear Sir,
I ran CFSAN SNP pipeline with given command
cfsan_snp_pipeline run -c snppipeline.conf -s samples/ reference/lambda_virus.fasta

in my laptop.  I got he following error messages.

 

# Command : /home/swamy123/.local/bin/cfsan_snp_pipeline map_reads --threads 4 reference/lambda_virus.fasta samples/sample3/sample3_1.fastq samples/sample3/sample3_2.fastq
# Working Directory : /home/swamy123/Desktop/swamy/test/lambdaVirusInputs
# Hostname : swamy123-Inspiron-N5110
# RAM : 3,842 MB
# Python Version : 2.7.17 (default, Nov 7 2019, 10:07:09) [GCC 7.4.0]
# Program Version : cfsan_snp_pipeline map_reads 2.1.1

# 2020-04-24 02:55:47 cfsan_snp_pipeline map_reads --threads 4 reference/lambda_virus.fasta samples/sample3/sample3_1.fastq samples/sample3/sample3_2.fastq
Options:
forceFlag=False
referenceFile=reference/lambda_virus.fasta
sampleFastqFile1=samples/sample3/sample3_1.fastq
sampleFastqFile2=samples/sample3/sample3_2.fastq
threads=4
verbose=1

# sample3 has already been aligned to lambda_virus. Use the -f option to force a rebuild.
# Unsorted bam file is already freshly created for sample3. Use the -f option to force a rebuild.
# Sorted bam file is already freshly created for sample3. Use the -f option to force a rebuild.
# Deduped bam file is already freshly created for sample3. Use the -f option to force a rebuild.
# Bam file index is already freshly created for sample3. Use the -f option to force a rebuild.
# Realign targets file is already freshly created for sample3. Use the -f option to force a rebuild.
# Realign around indels
# 2020-04-24 02:55:50 java -Xmx3500m -jar /home/swamy123/softwares/GenomeAnalysisTK/GenomeAnalysisTK.jar HaplotypeCaller -R reference/lambda_virus.fasta -targetIntervals samples/sample3/realign.target.intervals -I samples/sample3/reads.sorted.deduped.bam -O samples/sample3/reads.sorted.deduped.indelrealigned.bam
# GATK version 2.21.2
USAGE: HaplotypeCaller [arguments]

Call germline SNPs and indels via local re-assembly of haplotypes
Version:4.1.6.0

Required Arguments:

--input,-I:String 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:String 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_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, 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:
{AlleleSpecificAnnotation, 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, DepthPerSampleHC, 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.

--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.

--correct-overlapping-quality:Boolean
Undocumented option Default value: false. Possible values: {true, false}

--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, 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.

--gcs-project-for-requester-pays:String
Project to bill when accessing "requester pays" buckets. If unset, these buckets cannot be
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: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}

--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,
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}

--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:GATKPathSpecifier 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-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].

--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:DoubleLn likelihood ratio threshold for adaptive pruning algorithm Default value:
2.302585092994046.

--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 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.

--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:StringA 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 conjuction 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 conjuction with
argument(s) minimumLeadingTrailingSoftClippedRatio

***********************************************************************

A USER ERROR has occurred: t is not a recognized option

***********************************************************************
Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace.
Error occured while running:
java -Xmx3500m -jar /home/swamy123/softwares/GenomeAnalysisTK/GenomeAnalysisTK.jar HaplotypeCaller -R reference/lambda_virus.fasta -targetIntervals samples/sample3/realign.target.intervals -I samples/sample3/reads.sorted.deduped.bam -O samples/sample3/reads.sorted.deduped.indelrealigned.bam