BETA StructuralVariationDiscoveryPipelineSpark

Runs the structural variation discovery workflow on a single sample

Category Structural Variant Discovery

Overview

Runs the structural variation discovery workflow on a single sample

This tool packages the algorithms described in {@link FindBreakpointEvidenceSpark} and {@link org.broadinstitute.hellbender.tools.spark.sv.discovery.DiscoverVariantsFromContigAlignmentsSAMSpark} as an integrated workflow. Please consult the descriptions of those tools for more details about the algorithms employed. In brief, input reads are examined for evidence of structural variation in a genomic region, regions so identified are locally assembled, and the local assemblies are called for structural variation.

Inputs

An input file of aligned reads.
The reference to which the reads have been aligned.
A BWA index image for the reference. You can use BwaMemIndexImageCreator to create the index image file.
A list of ubiquitous kmers to ignore. You can use FindBadGenomicGenomicKmersSpark to create the list of kmers to ignore.

Output

A sam file with all of the contigs generated by local assemblies aligned to reference.
A vcf file describing the discovered structural variants.

Optional Output

Extra, optional output is generated when the experimental interpretation unit is run (note that they may change as features are still being experimented and added)

several VCF files containing variants discovered via different code path (ultimately will be merged into a single VCF)
query name sorted SAM file of local assembly contigs from whose alignments we can not yet make un-ambiguous calls (intended for debugging and future developments)

Usage example

   gatk StructuralVariationDiscoveryPipelineSpark \
     -I input_reads.bam \
     -R reference.2bit \
     --aligner-index-image reference.img \
     --kmers-to-ignore kmers_to_ignore.txt \
     --contig-sam-file aligned_contigs.sam \
     -O structural_variants.vcf

This tool can be run without explicitly specifying Spark options. That is to say, the given example command without Spark options will run locally. See Tutorial#10060 for an example of how to set up and run a Spark tool on a cloud Spark cluster.

Caveats

Expected input is a paired-end, coordinate-sorted BAM with around 30x coverage. Coverage much lower than that probably won't work well.

The reference is broadcast by Spark, and must therefore be a .2bit file due to current restrictions.

Additional Information

Read filters

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

WellformedReadFilter

StructuralVariationDiscoveryPipelineSpark 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
--aligner-index-image		bwa-mem index image file
--contig-sam-file		sam file for aligned contigs
--input -I		BAM/SAM/CRAM file containing reads
--kmers-to-ignore		file containing ubiquitous kmer list. see FindBadGenomicKmersSpark to generate it.
--output -O		directory for VCF output, including those from experimental interpretation tool if so requested, will be created if not present; sample name will be appended after the provided argument
--reference -R		Reference sequence file
Optional Tool Arguments
--adapter-sequence		Adapter sequence.
--allowed-short-fragment-overhang	10	Proper pairs have the positive strand read upstream of the negative strand read, but we allow this much slop for short fragments.
--arguments_file		read one or more arguments files and add them to the command line
--assembled-contigs-output-order -sort	coordinate	sorting order to be used for the output assembly alignments SAM/BAM file (currently only coordinate or query name is supported)
--assembly-imprecise-evidence-overlap-uncertainty	100	Uncertainty in overlap of assembled breakpoints and evidence target links.
--assembly-to-mapped-size-ratio-guess	7	Guess at the ratio of reads in the final assembly to the number reads mapped to the interval.
--bam-partition-size	0	maximum number of bytes to read from a file into each partition of reads. Setting this higher will result in fewer partitions. Note that this will not be equal to the size of the partition in memory. Defaults to 0, which uses the default split size (determined by the Hadoop input format, typically the size of one HDFS block).
--breakpoint-evidence-dir		directory for evidence output
--breakpoint-intervals		file for breakpoint intervals output
--cleaner-max-copy-number	4	KmerCleaner maximum copy number (not count, but copy number) for a kmer. Kmers observed too frequently are probably mismapped or ubiquitous.
--cleaner-max-intervals	3	KmerCleaner maximum number of intervals for a localizing kmer. If a kmer occurs in too many intervals, it isn't sufficiently local.
--cleaner-min-kmer-count	4	KmerCleaner minimum kmer count for a localizing kmer. If we see it less often than this many times, we're guessing it's erroneous.
--cnv-calls		External CNV calls file. Should be single sample VCF, and contain only confident autosomal non-reference CNV calls (for now).
--conf		Spark properties to set on the Spark context in the format =
--cross-contigs-to-ignore		file containing alt contig names that will be ignored when looking for inter-contig pairs
--disable-sequence-dictionary-validation	false	If specified, do not check the sequence dictionaries from our inputs for compatibility. Use at your own risk!
--exclusion-interval-padding	0	Exclusion interval padding.
--exclusion-intervals		file of reference intervals to exclude
--external-evidence		external evidence input file
--external-evidence-uncertainty	150	Uncertainty in location of external evidence.
--external-evidence-weight	10	Weight to give external evidence.
--fastq-dir		output dir for assembled fastqs
--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.
--help -h	false	display the help message
--high-coverage-intervals		file for high-coverage intervals output
--high-depth-coverage-factor	3	We filter out contiguous regions of the genome that have coverage of at least high-depth-coverage-factor * avg-coverage and a peak coverage of high-depth-coverage-peak-factor * avg-coverage, because the reads mapped to those regions tend to be non-local and high depth prevents accurate assembly.
--high-depth-coverage-peak-factor	7	We filter out contiguous regions of the genome that have coverage of at least high-depth-coverage-factor * avg-coverage and a peak coverage of high-depth-coverage-peak-factor * avg-coverage, because the reads mapped to those regions tend to be non-local and high depth prevents accurate assembly.
--imprecise-variant-evidence-threshold	7	Number of pieces of imprecise evidence necessary to call a variant in the absence of an assembled breakpoint.
--include-mapping-location	true	Include read mapping location in FASTQ files.
--interval-merging-rule -imr	ALL	Interval merging rule for abutting intervals
--interval-only-assembly	false	Don't look for extra reads mapped outside the interval.
--intervals -L		One or more genomic intervals over which to operate
--k-size	51	Kmer size.
--kmer-intervals		file for kmer intervals output
--kmer-max-dust-score	49	Maximum kmer DUST score.
--max-callable-imprecise-deletion-size	15000	Maximum size deletion to call based on imprecise evidence without corroborating read depth evidence
--max-fastq-size	3000000	Maximum total bases in FASTQs that can be assembled.
--max-tracked-fragment-length	2000	Largest fragment size that will be explicitly counted in determining fragment size statistics.
--min-align-length	50	Minimum flanking alignment length
--min-coherent-evidence-coverage-ratio	0.1633408753260167	Minimum weight of the evidence that shares a distal target locus to validate the evidence, as a ratio of the mean coverage in the BAM. The default value is coherent-count / mean coverage ~ 7 / 42.9 ~ 0.163
--min-evidence-coverage-ratio	0.35001616141289293	Minimum weight of the corroborating read evidence to validate some single piece of evidence, as a ratio of the mean coverage in the BAM. The default value is overlap-count / mean coverage ~ 15 / 42.9 ~ 0.350
--min-evidence-mapq	20	The minimum mapping quality for reads used to gather evidence of breakpoints.
--min-evidence-match-length	45	The minimum length of the matched portion of an interesting alignment. Reads that don't match at least this many reference bases won't be used in gathering evidence.
--min-kmers-per-interval	5	Minimum number of localizing kmers in a valid interval.
--min-mq -mq	30	Minimum mapping quality of evidence assembly contig
--num-reducers	0	For tools that shuffle data or write an output, sets the number of reducers. Defaults to 0, which gives one partition per 10MB of input.
--output-shard-tmp-dir		when writing a bam, in single sharded mode this directory to write the temporary intermediate output shards, if not specified .parts/ will be used
--program-name		Name of the program running
--qname-intervals-for-assembly		file for mapped qname intervals output
--qname-intervals-mapped		file for mapped qname intervals output
--read-metadata		output file for read metadata
--run-without-gaps-annotation	false	Allow evidence filter to run without gaps annotation (assume no gaps).
--run-without-umap-s100-annotation	false	Allow evidence filter to run without annotation for single-read mappability of 100-mers (assume all mappable).
--sharded-output	false	For tools that write an output, write the output in multiple pieces (shards)
--spark-master	local[*]	URL of the Spark Master to submit jobs to when using the Spark pipeline runner.
--spark-verbosity		Spark verbosity. Overrides --verbosity for Spark-generated logs only. Possible values: {ALL, DEBUG, INFO, WARN, ERROR, FATAL, OFF, TRACE}
--sv-evidence-filter-model-file		Path to xgboost classifier model file for evidence filtering
--sv-evidence-filter-threshold-probability	0.92	Minimum classified probability for a piece of evidence to pass xgboost evidence filter
--sv-genome-gaps-file		Path to file enumerating gaps in the reference genome, used by classifier to score evidence for filtering. To use classifier without specifying gaps file, pass the flag --run-without-gaps-annotation
--sv-genome-umap-s100-file		Path to single read 100-mer mappability file in the reference genome, used by classifier to score evidence for filtering. To use classifier without specifying mappability file, pass the flag --run-without-umap-s100-annotation
--target-link-file		output file for non-assembled breakpoints in bedpe format
--truth-interval-padding	50	Breakpoint padding for evaluation against truth data.
--unfiltered-breakpoint-evidence-dir		directory for evidence output
--use-nio	false	Whether to use NIO or the Hadoop filesystem (default) for reading files. (Note that the Hadoop filesystem is always used for writing files.)
--version	false	display the version number for this tool
--write-gfas	false	Write GFA representation of assemblies in fastq-dir.
Optional Common Arguments
--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 index when writing a coordinate-sorted BAM file.
--create-output-bam-splitting-index	true	If true, create a BAM splitting index (SBI) when writing a coordinate-sorted BAM file.
--create-output-variant-index -OVI	true	If true, create a VCF index when writing a coordinate-sorted VCF file.
--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).
--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.
--splitting-index-granularity	4096	Granularity to use when writing a splitting index, one entry will be put into the index every n reads where n is this granularity value. Smaller granularity results in a larger index with more available split points.
--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
--debug-mode	false	Run interpretation tool in debug mode (more information print to screen)
--exp-interpret	false	flag to signal that user wants to run experimental interpretation tool as well
--expand-assembly-graph	true	Traverse assembly graph and produce contigs for all paths.
--pop-variant-bubbles	false	Aggressively simplify local assemblies, ignoring small variants.
--remove-shadowed-contigs	true	Simplify local assemblies by removing contigs shadowed by similar contigs.
--showHidden	false	display hidden arguments
--z-dropoff	20	ZDropoff (see Bwa mem manual) for contig alignment.

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.

--adapter-sequence

Adapter sequence.

String null

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

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

boolean true

--aligner-index-image

bwa-mem index image file

R String null

--allowed-short-fragment-overhang

Proper pairs have the positive strand read upstream of the negative strand read, but we allow this much slop for short fragments.

int 10 [ [ -∞ ∞ ] ]

--arguments_file

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

List[File] []

--assembled-contigs-output-order / -sort

sorting order to be used for the output assembly alignments SAM/BAM file (currently only coordinate or query name is supported)

The --assembled-contigs-output-order argument is an enumerated type (SortOrder), which can have one of the following values:

unsorted
queryname
coordinate
duplicate
unknown

SortOrder coordinate

--assembly-imprecise-evidence-overlap-uncertainty

Uncertainty in overlap of assembled breakpoints and evidence target links.

int 100 [ [ -∞ ∞ ] ]

--assembly-to-mapped-size-ratio-guess

Guess at the ratio of reads in the final assembly to the number reads mapped to the interval.

int 7 [ [ -∞ ∞ ] ]

--bam-partition-size

maximum number of bytes to read from a file into each partition of reads. Setting this higher will result in fewer partitions. Note that this will not be equal to the size of the partition in memory. Defaults to 0, which uses the default split size (determined by the Hadoop input format, typically the size of one HDFS block).

long 0 [ [ -∞ ∞ ] ]

--breakpoint-evidence-dir

directory for evidence output

String null

--breakpoint-intervals

file for breakpoint intervals output

String null

--cleaner-max-copy-number

KmerCleaner maximum copy number (not count, but copy number) for a kmer. Kmers observed too frequently are probably mismapped or ubiquitous.

int 4 [ [ -∞ ∞ ] ]

--cleaner-max-intervals

KmerCleaner maximum number of intervals for a localizing kmer. If a kmer occurs in too many intervals, it isn't sufficiently local.

int 3 [ [ -∞ ∞ ] ]

--cleaner-min-kmer-count

KmerCleaner minimum kmer count for a localizing kmer. If we see it less often than this many times, we're guessing it's erroneous.

int 4 [ [ -∞ ∞ ] ]

--cnv-calls

External CNV calls file. Should be single sample VCF, and contain only confident autosomal non-reference CNV calls (for now).

String null

--conf

Spark properties to set on the Spark context in the format =

List[String] []

--contig-sam-file

sam file for aligned contigs

R String null

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

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

boolean true

--create-output-bam-splitting-index

If true, create a BAM splitting index (SBI) when writing a coordinate-sorted BAM file.

boolean true

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

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

boolean true

--cross-contigs-to-ignore

file containing alt contig names that will be ignored when looking for inter-contig pairs
This is a path to a text file of contig names (one per line) that will be ignored when looking for inter-contig pairs.

String null

--debug-mode

Run interpretation tool in debug mode (more information print to screen)

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-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

--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] []

--exclusion-interval-padding

Exclusion interval padding.

int 0 [ [ -∞ ∞ ] ]

--exclusion-intervals

file of reference intervals to exclude
This is a file that calls out the coordinates of intervals in the reference assembly to exclude from consideration when calling putative breakpoints. Each line is a tab-delimited interval with 1-based inclusive coordinates like this: chr1 124535434 142535434

String null

--exp-interpret

flag to signal that user wants to run experimental interpretation tool as well

Boolean false

--expand-assembly-graph

Traverse assembly graph and produce contigs for all paths.

boolean true

--external-evidence

external evidence input file

String null

--external-evidence-uncertainty

Uncertainty in location of external evidence.

int 150 [ [ -∞ ∞ ] ]

--external-evidence-weight

Weight to give external evidence.

int 10 [ [ -∞ ∞ ] ]

--fastq-dir

output dir for assembled fastqs

String null

--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 ""

--help / -h

display the help message

boolean false

--high-coverage-intervals

file for high-coverage intervals output

String null

--high-depth-coverage-factor

We filter out contiguous regions of the genome that have coverage of at least high-depth-coverage-factor * avg-coverage and a peak coverage of high-depth-coverage-peak-factor * avg-coverage, because the reads mapped to those regions tend to be non-local and high depth prevents accurate assembly.

int 3 [ [ -∞ ∞ ] ]

--high-depth-coverage-peak-factor

int 7 [ [ -∞ ∞ ] ]

--imprecise-variant-evidence-threshold

Number of pieces of imprecise evidence necessary to call a variant in the absence of an assembled breakpoint.

int 7 [ [ -∞ ∞ ] ]

--include-mapping-location

Include read mapping location in FASTQ files.

boolean true

--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-only-assembly

Don't look for extra reads mapped outside the interval.

boolean false

--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] []

--k-size

Kmer size.

int 51 [ [ -∞ ∞ ] ]

--kmer-intervals

file for kmer intervals output

String null

--kmer-max-dust-score

Maximum kmer DUST score.

int 49 [ [ -∞ ∞ ] ]

--kmers-to-ignore

file containing ubiquitous kmer list. see FindBadGenomicKmersSpark to generate it.
This is a path to a file of kmers that appear too frequently in the reference to be usable as probes to localize reads. We don't calculate it here, because it depends only on the reference. The program FindBadGenomicKmersSpark can produce such a list for you.

R String null

--max-callable-imprecise-deletion-size

Maximum size deletion to call based on imprecise evidence without corroborating read depth evidence

int 15000 [ [ -∞ ∞ ] ]

--max-fastq-size

Maximum total bases in FASTQs that can be assembled.

int 3000000 [ [ -∞ ∞ ] ]

--max-tracked-fragment-length

Largest fragment size that will be explicitly counted in determining fragment size statistics.

int 2000 [ [ -∞ ∞ ] ]

--min-align-length

Minimum flanking alignment length

Integer 50 [ [ -∞ ∞ ] ]

--min-coherent-evidence-coverage-ratio

Minimum weight of the evidence that shares a distal target locus to validate the evidence, as a ratio of the mean coverage in the BAM. The default value is coherent-count / mean coverage ~ 7 / 42.9 ~ 0.163

double 0.1633408753260167 [ [ -∞ ∞ ] ]

--min-evidence-coverage-ratio

Minimum weight of the corroborating read evidence to validate some single piece of evidence, as a ratio of the mean coverage in the BAM. The default value is overlap-count / mean coverage ~ 15 / 42.9 ~ 0.350

double 0.35001616141289293 [ [ -∞ ∞ ] ]

--min-evidence-mapq

The minimum mapping quality for reads used to gather evidence of breakpoints.

int 20 [ [ -∞ ∞ ] ]

--min-evidence-match-length

The minimum length of the matched portion of an interesting alignment. Reads that don't match at least this many reference bases won't be used in gathering evidence.

int 45 [ [ -∞ ∞ ] ]

--min-kmers-per-interval

Minimum number of localizing kmers in a valid interval.

int 5 [ [ -∞ ∞ ] ]

--min-mq / -mq

Minimum mapping quality of evidence assembly contig

Integer 30 [ [ -∞ ∞ ] ]

--num-reducers

For tools that shuffle data or write an output, sets the number of reducers. Defaults to 0, which gives one partition per 10MB of input.

int 0 [ [ -∞ ∞ ] ]

--output / -O

directory for VCF output, including those from experimental interpretation tool if so requested, will be created if not present; sample name will be appended after the provided argument

R String null

--output-shard-tmp-dir

when writing a bam, in single sharded mode this directory to write the temporary intermediate output shards, if not specified .parts/ will be used

Exclusion: This argument cannot be used at the same time as sharded-output.

String null

--pop-variant-bubbles

Aggressively simplify local assemblies, ignoring small variants.

boolean false

--program-name

Name of the program running

String null

--qname-intervals-for-assembly

file for mapped qname intervals output

String null

--qname-intervals-mapped

file for mapped qname intervals output

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-metadata

output file for read metadata

String null

--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 file

R GATKPath null

--remove-shadowed-contigs

Simplify local assemblies by removing contigs shadowed by similar contigs.

boolean true

--run-without-gaps-annotation

Allow evidence filter to run without gaps annotation (assume no gaps).

boolean false

--run-without-umap-s100-annotation

Allow evidence filter to run without annotation for single-read mappability of 100-mers (assume all mappable).

boolean false

--sharded-output

For tools that write an output, write the output in multiple pieces (shards)

Exclusion: This argument cannot be used at the same time as output-shard-tmp-dir.

boolean false

--showHidden / -showHidden

display hidden arguments

boolean false

--spark-master

URL of the Spark Master to submit jobs to when using the Spark pipeline runner.

String local[*]

--spark-verbosity

Spark verbosity. Overrides --verbosity for Spark-generated logs only. Possible values: {ALL, DEBUG, INFO, WARN, ERROR, FATAL, OFF, TRACE}

String null

--splitting-index-granularity

Granularity to use when writing a splitting index, one entry will be put into the index every n reads where n is this granularity value. Smaller granularity results in a larger index with more available split points.

long 4096 [ [ 1 ∞ ] ]

--sv-evidence-filter-model-file

Path to xgboost classifier model file for evidence filtering

String null

--sv-evidence-filter-threshold-probability

Minimum classified probability for a piece of evidence to pass xgboost evidence filter

double 0.92 [ [ -∞ ∞ ] ]

--sv-genome-gaps-file

Path to file enumerating gaps in the reference genome, used by classifier to score evidence for filtering. To use classifier without specifying gaps file, pass the flag --run-without-gaps-annotation

String null

--sv-genome-umap-s100-file

Path to single read 100-mer mappability file in the reference genome, used by classifier to score evidence for filtering. To use classifier without specifying mappability file, pass the flag --run-without-umap-s100-annotation

String null

--target-link-file

output file for non-assembled breakpoints in bedpe format

String null

--tmp-dir

Temp directory to use.

GATKPath null

--truth-interval-padding

Breakpoint padding for evaluation against truth data.

int 50 [ [ -∞ ∞ ] ]

--unfiltered-breakpoint-evidence-dir

directory for evidence output

String 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-nio

Whether to use NIO or the Hadoop filesystem (default) for reading files. (Note that the Hadoop filesystem is always used for writing files.)

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

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

**BETA** StructuralVariationDiscoveryPipelineSpark

Category Structural Variant Discovery

Overview

Inputs

Output

Optional Output

Usage example

Caveats

Additional Information

Read filters

StructuralVariationDiscoveryPipelineSpark specific arguments

Argument details

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

--assembled-contigs-output-order / -sort

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

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

--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

--inverted-read-filter / -XRF

--min-mq / -mq

--output / -O

--read-filter / -RF

--read-index / -read-index

--read-validation-stringency / -VS

--reference / -R

--showHidden / -showHidden

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

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

--verbosity / -verbosity

BETA StructuralVariationDiscoveryPipelineSpark