GroundTruthReadsBuilder (EXPERIMENTAL) – GATK

Produces a flexible and robust ground truth set for base calling training

Category Flow Based Tools

Traversal ReadWalker

Overview

An internal tool to produce a flexible and robust ground truth set for base calling training.

Input

Coordinate-sorted and indexed SAM/BAM/CRAM
Maternal and Parental references (fa)
Folder with address translation files from reference to maternal/parental references (filename example: maternal.chr9.csv)

Output

CSV file containing maternal/parental haplotype scores and many more columns (.csv or .csv.gz supported)

At present, the output will contain the following columns (not nessarily in this order) for each processed read:

ReadName, ReadChrom, ReadStart, ReadEnd, tm, mapq, flags, ReadCigar, ReadSequence, ReadUnclippedStart, ReadUnclippedEnd - information directly extracted from the input read
PaternalHaplotypeInterval, BestHaplotypeSequence, PaternalHaplotypeScore - parental haplotype information. First the read interval is translated into parental space, the haplotype sequence extracted and then scored
Maternal* - same for maternal
RefHaplotypeScore - score computed from the reference haplotype
BestHaplotypeKey - flow based key for the 'best' (score wise) haplotype (out of the maternal/paternal) pair)
ConsensusHaplotypeKey - a flow based key constructed from the flow keys of the maternal and paternal haplotypes, containing only keys that agree (other keys filled with fixed/special value)

Usage examples

 gatk GroundTruthReadsBuilder \
  -R
  ../../../ref/Homo_sapiens_assembly38.fasta
  -I
  150548-UGAv3-4.chr9.cram
  --maternal-ref
  chr9_HG001_maternal.fa
  --paternal-ref
  chr9_HG001_paternal.fa
  --ancestral-translators-base-path
  ./
  --output-csv
  output-small.csv
  --subsampling-ratio
  1.0
  --max-output-reads
  100000000
  --intervals
  chr9:109991494-109991494
  --smith-waterman
  FASTEST_AVAILABLE
  --likelihood-calculation-engine
  FlowBased
  -mbq
  0
  --kmer-size
  10
  --gt-debug
  --output-flow-length
  1000
  --haplotype-output-padding-size
  8
  --prepend-sequence
  TTTT
  --append-sequence
  CCCC

Additional Information

Read filters

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

WellformedReadFilter

GroundTruthReadsBuilder 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
--ancestral-translators-base-path		base path for ancestral translation ancestral.contig.csv files
--input -I		BAM/SAM/CRAM file containing reads
--maternal-ref		maternal reference file
--output-csv		main CSV output file. the file containing maternal/parental maternal and paternal haplotype sequences and scores (and many more columns). supported file extensions: .csv, .csv.gz.
--paternal-ref		paternal reference file
Optional Tool Arguments
--append-sequence		Sequence to append (adapter)
--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!
--discard-non-polyt-softclipped-reads	false	Discard reads which are softclipped, unless the softclip is polyT, defaults to true
--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
--false-snp-compensation	false	skip haplotype bases until same base as read starts (false SNP compensation)
--fill-softclipped-reads	false	Softclipped reads should be filled from haplotype, otherwise (default) filled with -83
--fill-trimmed-reads	false	Reads with tm:Q or tm:Z should be filled from haplotype, otherwise (default) filled with -80
--fill-trimmed-reads-Q	false	Reads with tm:Q should be filled from haplotype, otherwise (default) filled with -80
--fill-trimmed-reads-Z	false	Reads with tm:Z should be filled from haplotype, otherwise (default) filled with -80
--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.
--gt-no-output	false	do not generate output records
--haplotype-output-padding-size	8	Number of N to append to best haplotype on output
--help -h	false	display the help message
--include-supp-align	false	Include supplementary alignments
--interval-merging-rule -imr	ALL	Interval merging rule for abutting intervals
--intervals -L		One or more genomic intervals over which to operate
--max-output-reads	20000000	maximal number of reads to output
--max-rq	0.0	Maximal read quality
--min-haplotype-score	0.0	Minimal score (likelihood) on either haplotype
--min-haplotype-score-delta	0.0	Minimal score (likelihood) delta between haplotypes
--min-mq	0.0	Minimal mapping quality
--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
--output-flow-length	0	Required length of output flows
--prepend-sequence		Sequence to prepend (barcode)
--reference -R		Reference sequence
--sites-only-vcf-output	false	If true, don't emit genotype fields when writing vcf file output.
--subsampling-ratio	1.0	subsampling ratio, should be between 0 and 1
--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
--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-probability-threshold	0.003	Lowest probability ratio to be used as an option
--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-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

--ancestral-translators-base-path

base path for ancestral translation ancestral.contig.csv files

R GATKPath null

--append-sequence

Sequence to append (adapter)

String null

--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

--discard-non-polyt-softclipped-reads

Discard reads which are softclipped, unless the softclip is polyT, defaults to true

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).

List[String] []

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

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

double 0.02 [ [ -∞ ∞ ] ]

--false-snp-compensation

skip haplotype bases until same base as read starts (false SNP compensation)

boolean false

--fill-softclipped-reads

Softclipped reads should be filled from haplotype, otherwise (default) filled with -83

boolean false

--fill-trimmed-reads

Reads with tm:Q or tm:Z should be filled from haplotype, otherwise (default) filled with -80

boolean false

--fill-trimmed-reads-Q

Reads with tm:Q should be filled from haplotype, otherwise (default) filled with -80

boolean false

--fill-trimmed-reads-Z

Reads with tm:Z should be filled from haplotype, otherwise (default) filled with -80

boolean false

--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-probability-threshold

Lowest probability ratio to be used as an option

double 0.003 [ [ -∞ ∞ ] ]

--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 ""

--gt-no-output

do not generate output records

boolean false

--haplotype-output-padding-size

Number of N to append to best haplotype on output

int 8 [ [ -∞ ∞ ] ]

--help / -h

display the help message

boolean false

--include-supp-align

Include supplementary alignments

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] []

--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

--maternal-ref

maternal reference file

R GATKPath null

--max-output-reads

maximal number of reads to output

int 20000000 [ [ -∞ ∞ ] ]

--max-rq

Maximal read quality

double 0.0 [ [ -∞ ∞ ] ]

--max-variants-per-shard

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

int 0 [ [ 0 ∞ ] ]

--min-haplotype-score

Minimal score (likelihood) on either haplotype

double 0.0 [ [ -∞ ∞ ] ]

--min-haplotype-score-delta

Minimal score (likelihood) delta between haplotypes

double 0.0 [ [ -∞ ∞ ] ]

--min-mq

Minimal mapping quality

double 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

--output-csv

main CSV output file. the file containing maternal/parental maternal and paternal haplotype sequences and scores (and many more columns). supported file extensions: .csv, .csv.gz.

R GATKPath null

--output-flow-length

Required length of output flows

int 0 [ [ -∞ ∞ ] ]

--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

--paternal-ref

paternal reference file

R 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 [ [ -∞ ∞ ] ]

--prepend-sequence

Sequence to prepend (barcode)

String null

--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

--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

--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

--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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GATK version 4.3.0.0 built at Wed, 12 Oct 2022 21:04:44 -0400.

Genome Analysis Toolkit

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Category Flow Based Tools

Traversal ReadWalker

Overview

Input

Output

Usage examples

Additional Information

Read filters

GroundTruthReadsBuilder specific arguments

Argument details

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

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

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

--cloud-prefetch-buffer / -CPB

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

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

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

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

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

--disable-read-filter / -DF

--disable-sequence-dictionary-validation / -disable-sequence-dictionary-validation

--disable-tool-default-read-filters / -disable-tool-default-read-filters

--exclude-intervals / -XL

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

--help / -h

--input / -I

--interval-exclusion-padding / -ixp

--interval-merging-rule / -imr

--interval-padding / -ip

--interval-set-rule / -isr

--intervals / -L

--lenient / -LE

--pair-hmm-implementation / -pairHMM

--read-filter / -RF

--read-index / -read-index

--read-validation-stringency / -VS

--reference / -R

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

--sequence-dictionary / -sequence-dictionary

--showHidden / -showHidden

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

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

--verbosity / -verbosity

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