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4.6.2.0

**EXPERIMENTAL** GroundTruthScorer

Score reads against a reference/ground truth

Category Flow Based Tools

Traversal ReadWalker

Overview

Converts Ultima reads into flow-based annotation, and provides some general statistics regarding quality and errors relative to the reference. Ultima data is flow-based, and thus the original computed quality refers to each flow, rather than each base. In the Ultima cram/bam, there is a per-base representation of the original flow qualities, where the original quality is distributed along each flow (homopolymer). In order to reconstitute the original flow information, the tool incorporates the information encoded in the Ultima cram/bam, and outputs both the read in flow space, as well as a conversion of the aligned reference portion into flow space, and an alignment score.

Input

Output

CSV Output Description

csv with the read representation in flow space. The csv includes the following columns:
  • ReadName
  • ReadKey : The signal of the read at each flow according to the flow order
  • ReadIsReversed : Whether the read is reversed in the alignment
  • ReadMQ : The mapping quality of the read
  • ReadRQ : The read rq value
  • GroundTruthKey : The aligned reference section, translated into per-flow signals
  • ReadSequence
  • Score : A flow-based alignment score. Since the alignment is per-flow, in the case that there\u2019s a cycle skip, the read and reference flow signals will not be aligned, and therefore the score will be inaccurate.
  • NormalizedScore: A flow-based normalized alignment score
  • ErrorProbability : The error of each flow (corresponds to the signals in ReadKey)
  • ReadKeyLength
  • GroundTruthKeyLength
  • CycleSkipStatus : One of NS (Non Skip), PCS (Possible Cycle Skip), or CS (Cycle Skip)
  • Cigar
  • LowestQBaseTP

    • GATK Report Description

    In the quality report (optional), the following tables are included:
  • qualReport:error rate per qual : The error rate for each quality. Columns:
  • qual_hmerReport:error rate per qual by hmer. The error rate for each quality and hmer combination. Columns:
  • qual_hmer_deviation_base_Report:error rate per qual by hmer and deviation. The count of errors for each qual, hmer, deviation and base
  • Phred/qual statistics per flow position report. Various statistics for each flow position in relationship to the found quality value. Columns:

    • Usage examples

     gatk GroundTruthScorer \
   -I input.bam \
   -R reference.fasta.gz
   -L chr20 \
   --output-csv output.csv \
   --report-file report.txt \
   --omit-zeros-from-report \ (optional)
   --features-file dbsnp.chr9.vcf.gz \ (optional)
   --genome-prior genome_prior.csv (optional)
    {@GATK.walkertype ReadWalker}

    Additional Information

    Read filters

    This Read Filter is automatically applied to the data by the Engine before processing by GroundTruthScorer.

    GroundTruthScorer specific arguments

    This table summarizes the command-line arguments that are specific to this tool. For more details on each argument, see the list further down below the table or click on an argument name to jump directly to that entry in the list.

    Argument name(s) Default value Summary
    Required Arguments
    --input
     -I     		BAM/SAM/CRAM file containing reads
    --output-csv
    		 main CSV output file. supported file extensions: .csv, .csv.gz.
    Optional Tool Arguments
    --add-mean-call
    		 false Add ReadMeanCall and ReadProbs columns to output
    --arguments_file
    		 read one or more arguments files and add them to the command line
    --base-quality-score-threshold
    		 18 Base qualities below this threshold will be reduced to the minimum (6)
    --cloud-index-prefetch-buffer
     -CIPB     		-1 Size of the cloud-only prefetch buffer (in MB; 0 to disable). Defaults to cloudPrefetchBuffer if unset.
    --cloud-prefetch-buffer
     -CPB     		40 Size of the cloud-only prefetch buffer (in MB; 0 to disable).
    --disable-bam-index-caching
     -DBIC     		false 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.
    --disable-sequence-dictionary-validation
    		 false If specified, do not check the sequence dictionaries from our inputs for compatibility. Use at your own risk!
    --dont-use-dragstr-pair-hmm-scores
    		 false disable DRAGstr pair-hmm score even when dragstr-params-path was provided
    --dragstr-het-hom-ratio
    		 2 het to hom prior ratio use with DRAGstr on
    --dragstr-params-path
    		 location of the DRAGstr model parameters for STR error correction used in the Pair HMM. When provided, it overrides other PCR error correcting mechanisms
    --enable-dynamic-read-disqualification-for-genotyping
    		 false Will enable less strict read disqualification low base quality reads
    --exclude-zero-flows
    		 false should flows with a call of zero be included in the percentile report?
    --features-file
    		 A VCF file containing features to be used as a use for filtering reads.
    --gcs-max-retries
     -gcs-retries     		20 If the GCS bucket channel errors out, how many times it will attempt to re-initiate the connection
    --gcs-project-for-requester-pays
    		 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.
    --genome-prior
    		 CSV input file containing genome-prior (one line per base with hmer frequencies).
    --gt-no-output
    		 false do not generate output records
    --help
     -h     		false display the help message
    --interval-merging-rule
     -imr     		ALL Interval merging rule for abutting intervals
    --intervals
     -L     		One or more genomic intervals over which to operate
    --native-pair-hmm-threads
    		 4 How many threads should a native pairHMM implementation use
    --native-pair-hmm-use-double-precision
    		 false use double precision in the native pairHmm. This is slower but matches the java implementation better
    --normalized-score-threshold
    		 -0.1 threshold for normalized score, below which reads are ignored
    --omit-zeros-from-report
    		 false omit zero values from output report
    --quality-percentiles
    		 10,25,50,75,90 list of quality percentiles, defaults to 10,25,50,75,90
    --reference
     -R     		Reference sequence
    --report-file
    		 report output file.
    --sites-only-vcf-output
    		 false If true, don't emit genotype fields when writing vcf file output.
    --use-softclipped-bases
    		 false
    --version
    		 false display the version number for this tool
    Optional Common Arguments
    --add-output-sam-program-record
    		 true If true, adds a PG tag to created SAM/BAM/CRAM files.
    --add-output-vcf-command-line
    		 true If true, adds a command line header line to created VCF files.
    --create-output-bam-index
     -OBI     		true If true, create a BAM/CRAM index when writing a coordinate-sorted BAM/CRAM file.
    --create-output-bam-md5
     -OBM     		false If true, create a MD5 digest for any BAM/SAM/CRAM file created
    --create-output-variant-index
     -OVI     		true If true, create a VCF index when writing a coordinate-sorted VCF file.
    --create-output-variant-md5
     -OVM     		false If true, create a a MD5 digest any VCF file created.
    --disable-read-filter
     -DF     		Read filters to be disabled before analysis
    --disable-tool-default-read-filters
    		 false Disable all tool default read filters (WARNING: many tools will not function correctly without their default read filters on)
    --exclude-intervals
     -XL     		One or more genomic intervals to exclude from processing
    --gatk-config-file
    		 A configuration file to use with the GATK.
    --interval-exclusion-padding
     -ixp     		0 Amount of padding (in bp) to add to each interval you are excluding.
    --interval-padding
     -ip     		0 Amount of padding (in bp) to add to each interval you are including.
    --interval-set-rule
     -isr     		UNION Set merging approach to use for combining interval inputs
    --inverted-read-filter
     -XRF     		Inverted (with flipped acceptance/failure conditions) read filters applied before analysis (after regular read filters).
    --lenient
     -LE     		false Lenient processing of VCF files
    --max-variants-per-shard
    		 0 If non-zero, partitions VCF output into shards, each containing up to the given number of records.
    --QUIET
    		 false Whether to suppress job-summary info on System.err.
    --read-filter
     -RF     		Read filters to be applied before analysis
    --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.
    --read-validation-stringency
     -VS     		SILENT 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.
    --seconds-between-progress-updates
    		 10.0 Output traversal statistics every time this many seconds elapse
    --sequence-dictionary
    		 Use the given sequence dictionary as the master/canonical sequence dictionary. Must be a .dict file.
    --tmp-dir
    		 Temp directory to use.
    --use-jdk-deflater
     -jdk-deflater     		false Whether to use the JdkDeflater (as opposed to IntelDeflater)
    --use-jdk-inflater
     -jdk-inflater     		false Whether to use the JdkInflater (as opposed to IntelInflater)
    --verbosity
    		 INFO Control verbosity of logging.
    Advanced Arguments
    --disable-cap-base-qualities-to-map-quality
    		 false If false this disables capping of base qualities in the HMM to the mapping quality of the read
    --disable-symmetric-hmm-normalizing
    		 false Toggle to revive legacy behavior of asymmetrically normalizing the arguments to the reference haplotype
    --expected-mismatch-rate-for-read-disqualification
    		 0.02 Error rate used to set expectation for post HMM read disqualification based on mismatches
    --flow-disallow-probs-larger-than-call
    		 false Cap probabilities of error to 1 relative to base call
    --flow-fill-empty-bins-value
    		 0.001 Value to fill the zeros of the matrix with
    --flow-lump-probs
    		 false Should all probabilities of insertion or deletion in the flow be combined together
    --flow-matrix-mods
    		 Modifications instructions to the read flow matrix. Format is src,dst{,src,dst}+. Example: 10,12,11,12 - these instructions will copy element 10 into 11 and 12
    --flow-probability-scaling-factor
    		 10 probability scaling factor for (phred=10) for probability quantization
    --flow-quantization-bins
    		 121 Number of bins for probability quantization
    --flow-remove-non-single-base-pair-indels
    		 false Should the probabilities of more then 1 indel be used
    --flow-remove-one-zero-probs
    		 false Remove probabilities of basecall of zero from non-zero genome
    --flow-report-insertion-or-deletion
    		 false Report either insertion or deletion, probability, not both
    --flow-retain-max-n-probs-base-format
    		 false Keep only hmer/2 probabilities (like in base format)
    --flow-symmetric-indel-probs
    		 false Should indel probabilities be symmetric in flow
    --flow-use-t0-tag
    		 false Use t0 tag if exists in the read to create flow matrix
    --keep-boundary-flows
    		 false prevent spreading of boundary flows.
    --likelihood-calculation-engine
    		 PairHMM What likelihood calculation engine to use to calculate the relative likelihood of reads vs haplotypes
    --pair-hmm-gap-continuation-penalty
    		 10 Flat gap continuation penalty for use in the Pair HMM
    --pair-hmm-implementation
     -pairHMM     		FASTEST_AVAILABLE The PairHMM implementation to use for genotype likelihood calculations
    --pair-hmm-results-file
    		 File to write exact pairHMM inputs/outputs to for debugging purposes
    --pcr-indel-model
    		 CONSERVATIVE The PCR indel model to use
    --phred-scaled-global-read-mismapping-rate
    		 45 The global assumed mismapping rate for reads
    --showHidden
    		 false display hidden arguments

    Argument details

    Arguments in this list are specific to this tool. Keep in mind that other arguments are available that are shared with other tools (e.g. command-line GATK arguments); see Inherited arguments above.

    --add-mean-call

    Add ReadMeanCall and ReadProbs columns to output

    boolean  false

    --add-output-sam-program-record / -add-output-sam-program-record

    If true, adds a PG tag to created SAM/BAM/CRAM files.

    boolean  true

    --add-output-vcf-command-line / -add-output-vcf-command-line

    If true, adds a command line header line to created VCF files.

    boolean  true

    --arguments_file

    read one or more arguments files and add them to the command line

    List[File]  []

    --base-quality-score-threshold

    Base qualities below this threshold will be reduced to the minimum (6)
    Bases with a quality below this threshold will reduced to the minimum usable qualiy score (6).

    byte  18  [ [ -∞  ∞ ] ]

    --cloud-index-prefetch-buffer / -CIPB

    Size of the cloud-only prefetch buffer (in MB; 0 to disable). Defaults to cloudPrefetchBuffer if unset.

    int  -1  [ [ -∞  ∞ ] ]

    --cloud-prefetch-buffer / -CPB

    Size of the cloud-only prefetch buffer (in MB; 0 to disable).

    int  40  [ [ -∞  ∞ ] ]

    --create-output-bam-index / -OBI

    If true, create a BAM/CRAM index when writing a coordinate-sorted BAM/CRAM file.

    boolean  true

    --create-output-bam-md5 / -OBM

    If true, create a MD5 digest for any BAM/SAM/CRAM file created

    boolean  false

    --create-output-variant-index / -OVI

    If true, create a VCF index when writing a coordinate-sorted VCF file.

    boolean  true

    --create-output-variant-md5 / -OVM

    If true, create a a MD5 digest any VCF file created.

    boolean  false

    --disable-bam-index-caching / -DBIC

    If true, don't cache bam indexes, this will reduce memory requirements but may harm performance if many intervals are specified. Caching is automatically disabled if there are no intervals specified.

    boolean  false

    --disable-cap-base-qualities-to-map-quality

    If false this disables capping of base qualities in the HMM to the mapping quality of the read

    boolean  false

    --disable-read-filter / -DF

    Read filters to be disabled before analysis

    List[String]  []

    --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!

    boolean  false

    --disable-symmetric-hmm-normalizing

    Toggle to revive legacy behavior of asymmetrically normalizing the arguments to the reference haplotype

    boolean  false

    --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)

    boolean  false

    --dont-use-dragstr-pair-hmm-scores

    disable DRAGstr pair-hmm score even when dragstr-params-path was provided

    boolean  false

    --dragstr-het-hom-ratio

    het to hom prior ratio use with DRAGstr on

    int  2  [ [ -∞  ∞ ] ]

    --dragstr-params-path

    location of the DRAGstr model parameters for STR error correction used in the Pair HMM. When provided, it overrides other PCR error correcting mechanisms

    GATKPath  null

    --enable-dynamic-read-disqualification-for-genotyping

    Will enable less strict read disqualification low base quality reads
    If enabled, rather than disqualifying all reads over a threshold of minimum hmm scores we will instead choose a less strict and less aggressive cap for disqualification based on the read length and base qualities.

    boolean  false

    --exclude-intervals / -XL

    One or more genomic intervals to exclude from processing
    Use this argument to exclude certain parts of the genome from the analysis (like -L, but the opposite). This argument can be specified multiple times. You can use samtools-style intervals either explicitly on the command line (e.g. -XL 1 or -XL 1:100-200) or by loading in a file containing a list of intervals (e.g. -XL myFile.intervals). strings gathered from the command line -XL argument to be parsed into intervals to exclude

    List[String]  []

    --exclude-zero-flows

    should flows with a call of zero be included in the percentile report?

    boolean  false

    --expected-mismatch-rate-for-read-disqualification

    Error rate used to set expectation for post HMM read disqualification based on mismatches

    double  0.02  [ [ -∞  ∞ ] ]

    --features-file

    A VCF file containing features to be used as a use for filtering reads.

    FeatureDataSource[VariantContext]  null

    --flow-disallow-probs-larger-than-call

    Cap probabilities of error to 1 relative to base call

    boolean  false

    --flow-fill-empty-bins-value

    Value to fill the zeros of the matrix with

    double  0.001  [ [ -∞  ∞ ] ]

    --flow-lump-probs

    Should all probabilities of insertion or deletion in the flow be combined together

    boolean  false

    --flow-matrix-mods

    Modifications instructions to the read flow matrix. Format is src,dst{,src,dst}+. Example: 10,12,11,12 - these instructions will copy element 10 into 11 and 12

    String  null

    --flow-probability-scaling-factor

    probability scaling factor for (phred=10) for probability quantization

    int  10  [ [ -∞  ∞ ] ]

    --flow-quantization-bins

    Number of bins for probability quantization

    int  121  [ [ -∞  ∞ ] ]

    --flow-remove-non-single-base-pair-indels

    Should the probabilities of more then 1 indel be used

    boolean  false

    --flow-remove-one-zero-probs

    Remove probabilities of basecall of zero from non-zero genome

    boolean  false

    --flow-report-insertion-or-deletion

    Report either insertion or deletion, probability, not both

    boolean  false

    --flow-retain-max-n-probs-base-format

    Keep only hmer/2 probabilities (like in base format)

    boolean  false

    --flow-symmetric-indel-probs

    Should indel probabilities be symmetric in flow

    boolean  false

    --flow-use-t0-tag

    Use t0 tag if exists in the read to create flow matrix

    boolean  false

    --gatk-config-file

    A configuration file to use with the GATK.

    String  null

    --gcs-max-retries / -gcs-retries

    If the GCS bucket channel errors out, how many times it will attempt to re-initiate the connection

    int  20  [ [ -∞  ∞ ] ]

    --gcs-project-for-requester-pays

    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.

    String  ""

    --genome-prior

    CSV input file containing genome-prior (one line per base with hmer frequencies).

    GATKPath  null

    --gt-no-output

    do not generate output records

    boolean  false

    --help / -h

    display the help message

    boolean  false

    --input / -I

    BAM/SAM/CRAM file containing reads

    R List[GATKPath]  []

    --interval-exclusion-padding / -ixp

    Amount of padding (in bp) to add to each interval you are excluding.
    Use this to add padding to the intervals specified using -XL. For example, '-XL 1:100' with a padding value of 20 would turn into '-XL 1:80-120'. This is typically used to add padding around targets when analyzing exomes.

    int  0  [ [ -∞  ∞ ] ]

    --interval-merging-rule / -imr

    Interval merging rule for abutting intervals
    By default, the program merges abutting intervals (i.e. intervals that are directly side-by-side but do not actually overlap) into a single continuous interval. However you can change this behavior if you want them to be treated as separate intervals instead.

    The --interval-merging-rule argument is an enumerated type (IntervalMergingRule), which can have one of the following values:

    ALL
    OVERLAPPING_ONLY

    IntervalMergingRule  ALL

    --interval-padding / -ip

    Amount of padding (in bp) to add to each interval you are including.
    Use this to add padding to the intervals specified using -L. For example, '-L 1:100' with a padding value of 20 would turn into '-L 1:80-120'. This is typically used to add padding around targets when analyzing exomes.

    int  0  [ [ -∞  ∞ ] ]

    --interval-set-rule / -isr

    Set merging approach to use for combining interval inputs
    By default, the program will take the UNION of all intervals specified using -L and/or -XL. However, you can change this setting for -L, for example if you want to take the INTERSECTION of the sets instead. E.g. to perform the analysis only on chromosome 1 exomes, you could specify -L exomes.intervals -L 1 --interval-set-rule INTERSECTION. However, it is not possible to modify the merging approach for intervals passed using -XL (they will always be merged using UNION). Note that if you specify both -L and -XL, the -XL interval set will be subtracted from the -L interval set.

    The --interval-set-rule argument is an enumerated type (IntervalSetRule), which can have one of the following values:

    UNION
    Take the union of all intervals
    INTERSECTION
    Take the intersection of intervals (the subset that overlaps all intervals specified)

    IntervalSetRule  UNION

    --intervals / -L

    One or more genomic intervals over which to operate

    List[String]  []

    --inverted-read-filter / -XRF

    Inverted (with flipped acceptance/failure conditions) read filters applied before analysis (after regular read filters).

    List[String]  []

    --keep-boundary-flows

    prevent spreading of boundary flows.

    boolean  false

    --lenient / -LE

    Lenient processing of VCF files

    boolean  false

    --likelihood-calculation-engine

    What likelihood calculation engine to use to calculate the relative likelihood of reads vs haplotypes

    The --likelihood-calculation-engine argument is an enumerated type (Implementation), which can have one of the following values:

    PairHMM
    Classic full pair-hmm all haplotypes vs all reads.
    FlowBased
    FlowBasedHMM

    Implementation  PairHMM

    --max-variants-per-shard

    If non-zero, partitions VCF output into shards, each containing up to the given number of records.

    int  0  [ [ 0  ∞ ] ]

    --native-pair-hmm-threads

    How many threads should a native pairHMM implementation use

    int  4  [ [ -∞  ∞ ] ]

    --native-pair-hmm-use-double-precision

    use double precision in the native pairHmm. This is slower but matches the java implementation better

    boolean  false

    --normalized-score-threshold

    threshold for normalized score, below which reads are ignored

    double  -0.1  [ [ -∞  ∞ ] ]

    --omit-zeros-from-report

    omit zero values from output report

    boolean  false

    --output-csv

    main CSV output file. supported file extensions: .csv, .csv.gz.

    R GATKPath  null

    --pair-hmm-gap-continuation-penalty

    Flat gap continuation penalty for use in the Pair HMM

    int  10  [ [ -∞  ∞ ] ]

    --pair-hmm-implementation / -pairHMM

    The PairHMM implementation to use for genotype likelihood calculations
    The PairHMM implementation to use for genotype likelihood calculations. The various implementations balance a tradeoff of accuracy and runtime.

    The --pair-hmm-implementation argument is an enumerated type (Implementation), which can have one of the following values:

    EXACT
    ORIGINAL
    LOGLESS_CACHING
    AVX_LOGLESS_CACHING
    AVX_LOGLESS_CACHING_OMP
    FASTEST_AVAILABLE

    Implementation  FASTEST_AVAILABLE

    --pair-hmm-results-file

    File to write exact pairHMM inputs/outputs to for debugging purposes
    Argument for generating a file of all of the inputs and outputs for the pair hmm

    GATKPath  null

    --pcr-indel-model

    The PCR indel model to use
    When calculating the likelihood of variants, we can try to correct for PCR errors that cause indel artifacts. The correction is based on the reference context, and acts specifically around repetitive sequences that tend to cause PCR errors). The variant likelihoods are penalized in increasing scale as the context around a putative indel is more repetitive (e.g. long homopolymer). The correction can be disabling by specifying '-pcrModel NONE'; in that case the default base insertion/deletion qualities will be used (or taken from the read if generated through the BaseRecalibrator). VERY IMPORTANT: when using PCR-free sequencing data we definitely recommend setting this argument to NONE .

    The --pcr-indel-model argument is an enumerated type (PCRErrorModel), which can have one of the following values:

    NONE
    no specialized PCR error model will be applied; if base insertion/deletion qualities are present they will be used
    HOSTILE
    a most aggressive model will be applied that sacrifices true positives in order to remove more false positives
    AGGRESSIVE
    a more aggressive model will be applied that sacrifices true positives in order to remove more false positives
    CONSERVATIVE
    a less aggressive model will be applied that tries to maintain a high true positive rate at the expense of allowing more false positives

    PCRErrorModel  CONSERVATIVE

    --phred-scaled-global-read-mismapping-rate

    The global assumed mismapping rate for reads
    The phredScaledGlobalReadMismappingRate reflects the average global mismapping rate of all reads, regardless of their mapping quality. This term effects the probability that a read originated from the reference haplotype, regardless of its edit distance from the reference, in that the read could have originated from the reference haplotype but from another location in the genome. Suppose a read has many mismatches from the reference, say like 5, but has a very high mapping quality of 60. Without this parameter, the read would contribute 5 * Q30 evidence in favor of its 5 mismatch haplotype compared to reference, potentially enough to make a call off that single read for all of these events. With this parameter set to Q30, though, the maximum evidence against any haplotype that this (and any) read could contribute is Q30. Set this term to any negative number to turn off the global mapping rate.

    int  45  [ [ -∞  ∞ ] ]

    --quality-percentiles

    list of quality percentiles, defaults to 10,25,50,75,90

    String  10,25,50,75,90

    --QUIET

    Whether to suppress job-summary info on System.err.

    Boolean  false

    --read-filter / -RF

    Read filters to be applied before analysis

    List[String]  []

    --read-index / -read-index

    Indices to use for the read inputs. If specified, an index must be provided for every read input and in the same order as the read inputs. If this argument is not specified, the path to the index for each input will be inferred automatically.

    List[GATKPath]  []

    --read-validation-stringency / -VS

    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.

    The --read-validation-stringency argument is an enumerated type (ValidationStringency), which can have one of the following values:

    STRICT
    LENIENT
    SILENT

    ValidationStringency  SILENT

    --reference / -R

    Reference sequence

    GATKPath  null

    --report-file

    report output file.

    GATKPath  null

    --seconds-between-progress-updates / -seconds-between-progress-updates

    Output traversal statistics every time this many seconds elapse

    double  10.0  [ [ -∞  ∞ ] ]

    --sequence-dictionary / -sequence-dictionary

    Use the given sequence dictionary as the master/canonical sequence dictionary. Must be a .dict file.

    GATKPath  null

    --showHidden / -showHidden

    display hidden arguments

    boolean  false

    --sites-only-vcf-output

    If true, don't emit genotype fields when writing vcf file output.

    boolean  false

    --tmp-dir

    Temp directory to use.

    GATKPath  null

    --use-jdk-deflater / -jdk-deflater

    Whether to use the JdkDeflater (as opposed to IntelDeflater)

    boolean  false

    --use-jdk-inflater / -jdk-inflater

    Whether to use the JdkInflater (as opposed to IntelInflater)

    boolean  false

    --use-softclipped-bases


    boolean  false

    --verbosity / -verbosity

    Control verbosity of logging.

    The --verbosity argument is an enumerated type (LogLevel), which can have one of the following values:

    ERROR
    WARNING
    INFO
    DEBUG

    LogLevel  INFO

    --version

    display the version number for this tool

    boolean  false

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    See also General Documentation | Tool Docs Index Tool Documentation Index | Support Forum

    GATK version 4.6.2.0 built at Sun, 13 Apr 2025 13:21:43 -0400.