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**BETA** FindBreakpointEvidenceSpark

(Internal) Produces local assemblies of genomic regions that may harbor structural variants

Category Structural Variant Discovery


Overview

(Internal) Produces local assemblies of genomic regions that may harbor structural variants

This tool is used in development and should not be of interest to most researchers. It packages the identification of genomic regions that might contain structural variation and the generation of local assemblies of these regions as a separate tool, independent of the calling of structural variations from these assemblies. Most researchers will run StructuralVariationDiscoveryPipelineSpark, which both generates local assemblies of interesting genomic regions, and then calls structural variants from these assemblies.

This tool identifies genomic regions that may harbor structural variants by integrating evidence from split reads, discordant read pairs, template-length anomalies, and copy-number variation. It then prepares local assemblies of these regions for structural variant calling. In addition to the reads that align to these regions, reads sharing kmers (fixed-length subsequences) with the reads aligned in these regions are extracted to produce the local assemblies.

The local assemblies are done with FermiLite, and the assembled contigs are aligned to reference with BWA-MEM.

The output is a file of aligned contigs from local assemblies to be used in calling structural variants.

Inputs

  • A SAM/BAM/CRAM file of paired-end, aligned and coordinate-sorted reads.
  • 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 file of aligned contigs.

Usage example

   gatk FindBreakpointEvidenceSpark \
     -I input_reads.bam \
     --aligner-index-image reference.img \
     --kmers-to-ignore ignored_kmers.txt \
     -O assemblies.sam
 

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.


Additional Information

Read filters

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

FindBreakpointEvidenceSpark 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
null bwa-mem index image file
--input
 -I
[] BAM/SAM/CRAM file containing reads
--kmers-to-ignore
null file containing ubiquitous kmer list. see FindBadGenomicKmersSpark to generate it.
--output
 -O
null sam file for aligned contigs
Optional Tool Arguments
--adapter-sequence
null 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-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
null directory for evidence output
--breakpoint-intervals
null 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.
--conf
[] spark properties to set on the spark context in the format =
--cross-contigs-to-ignore
null 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
null file of reference intervals to exclude
--external-evidence
null 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
null 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.
--help
 -h
false display the help message
--high-coverage-intervals
null 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.
--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
null file for kmer intervals output
--kmer-max-dust-score
49 Maximum kmer DUST score.
--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-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.
--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
null 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
null Name of the program running
--qname-intervals-for-assembly
null file for mapped qname intervals output
--qname-intervals-mapped
null file for mapped qname intervals output
--read-metadata
null output file for read metadata
--reference
 -R
null Reference sequence
--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.
--sv-evidence-filter-model-file
null 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-evidence-filter-type
DENSITY Filter method for selecting evidence to group into Assembly Intervals
--sv-genome-gaps-file
null 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
null 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
null output file for non-assembled breakpoints in bedpe format
--unfiltered-breakpoint-evidence-dir
null directory for evidence output
--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
null 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
--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.
--tmp-dir
null 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
--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 / NA

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 / NA

bwa-mem index image file

R String  null


--allowed-short-fragment-overhang / NA

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 / NA

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-to-mapped-size-ratio-guess / NA

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

int  7  [ [ -∞  ∞ ] ]


--bam-partition-size / NA

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 / NA

directory for evidence output

String  null


--breakpoint-intervals / NA

file for breakpoint intervals output

String  null


--cleaner-max-copy-number / NA

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 / NA

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 / NA

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  [ [ -∞  ∞ ] ]


--conf / -conf

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

List[String]  []


--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 / NA

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 / NA

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


--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).

List[String]  []


--exclusion-interval-padding / NA

Exclusion interval padding.

int  0  [ [ -∞  ∞ ] ]


--exclusion-intervals / NA

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


--expand-assembly-graph / NA

Traverse assembly graph and produce contigs for all paths.

boolean  true


--external-evidence / NA

external evidence input file

String  null


--external-evidence-uncertainty / NA

Uncertainty in location of external evidence.

int  150  [ [ -∞  ∞ ] ]


--external-evidence-weight / NA

Weight to give external evidence.

int  10  [ [ -∞  ∞ ] ]


--fastq-dir / NA

output dir for assembled fastqs

String  null


--gatk-config-file / NA

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 / NA

Project to bill when accessing "requester pays" buckets. If unset, these buckets cannot be accessed.

String  ""


--help / -h

display the help message

boolean  false


--high-coverage-intervals / NA

file for high-coverage intervals output

String  null


--high-depth-coverage-factor / NA

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 / NA

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  7  [ [ -∞  ∞ ] ]


--include-mapping-location / NA

Include read mapping location in FASTQ files.

boolean  true


--input / -I

BAM/SAM/CRAM file containing reads

R List[String]  []


--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 / NA

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]  []


--k-size / NA

Kmer size.

int  51  [ [ -∞  ∞ ] ]


--kmer-intervals / NA

file for kmer intervals output

String  null


--kmer-max-dust-score / NA

Maximum kmer DUST score.

int  49  [ [ -∞  ∞ ] ]


--kmers-to-ignore / NA

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-fastq-size / NA

Maximum total bases in FASTQs that can be assembled.

int  3000000  [ [ -∞  ∞ ] ]


--max-tracked-fragment-length / NA

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

int  2000  [ [ -∞  ∞ ] ]


--min-coherent-evidence-coverage-ratio / NA

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 / NA

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 / NA

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

int  20  [ [ -∞  ∞ ] ]


--min-evidence-match-length / NA

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 / NA

Minimum number of localizing kmers in a valid interval.

int  5  [ [ -∞  ∞ ] ]


--num-reducers / NA

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

sam file for aligned contigs

R String  null


--output-shard-tmp-dir / NA

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 / NA

Aggressively simplify local assemblies, ignoring small variants.

boolean  false


--program-name / NA

Name of the program running

String  null


--qname-intervals-for-assembly / NA

file for mapped qname intervals output

String  null


--qname-intervals-mapped / NA

file for mapped qname intervals output

String  null


--QUIET / NA

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[String]  []


--read-metadata / NA

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

String  null


--remove-shadowed-contigs / NA

Simplify local assemblies by removing contigs shadowed by similar contigs.

boolean  true


--run-without-gaps-annotation / NA

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

boolean  false


--run-without-umap-s100-annotation / NA

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

boolean  false


--sharded-output / NA

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 / NA

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

String  local[*]


--sv-evidence-filter-model-file / NA

Path to xgboost classifier model file for evidence filtering

String  null


--sv-evidence-filter-threshold-probability / NA

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

double  0.92  [ [ -∞  ∞ ] ]


--sv-evidence-filter-type / NA

Filter method for selecting evidence to group into Assembly Intervals

The --sv-evidence-filter-type argument is an enumerated type (SvEvidenceFilterType), which can have one of the following values:

DENSITY
XGBOOST

SvEvidenceFilterType  DENSITY


--sv-genome-gaps-file / NA

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 / NA

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 / NA

output file for non-assembled breakpoints in bedpe format

String  null


--tmp-dir / NA

Temp directory to use.

String  null


--unfiltered-breakpoint-evidence-dir / NA

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


--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 / NA

display the version number for this tool

boolean  false


--write-gfas / NA

Write GFA representation of assemblies in fastq-dir.

boolean  false


--z-dropoff / NA

ZDropoff (see Bwa mem manual) for contig alignment.

int  20  [ [ -∞  ∞ ] ]


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