(Internal) Examines aligned contigs from local assemblies and calls structural variants or their breakpoints

Category Structural Variant Discovery

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Overview

(Internal) Examines aligned contigs from local assemblies and calls structural variants or their breakpoints

This is an experimental tool and should not be of interest to most researchers. It is a prototype of a method for calling structural variation from alignments of assembled contigs and is under active development. For a more stable method for this, please see DiscoverVariantsFromContigAlignmentsSAMSpark.

This tool takes a file containing the alignments of assembled contigs (typically the output file produced by FindBreakpointEvidenceSpark) and searches for split alignments or alignments with large gaps indicating the presence of structural variation breakpoints. The type of each variation is determined by analyzing the signatures of the split alignments, and are written to VCF files in the designated output directory.

Inputs

• An input file of assembled contigs aligned to reference.
• The reference to which the contigs have been aligned.

Output

• Text files describing the discovered structural variants and complex structural variants in the specified output directory.

Usage example

   gatk SvDiscoverFromLocalAssemblyContigAlignmentsSpark \
     -I assemblies.sam \
     -R reference.2bit \
     -O output_directory
 

Notes

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

SvDiscoverFromLocalAssemblyContigAlignmentsSpark 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  -O	null	prefix for output files (including VCF files and if enabled, the signaling assembly contig's alignments); sample name will be appended after the provided argument
--reference  -R	null	Reference sequence file
Optional Tool Arguments
--arguments_file	[]	read one or more arguments files and add them to the command line
--assembly-imprecise-evidence-overlap-uncertainty	100	Uncertainty in overlap of assembled breakpoints and evidence target links.
--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).
--cnv-calls	null	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 =
--disable-sequence-dictionary-validation	false	If specified, do not check the sequence dictionaries from our inputs for compatibility. Use at your own risk!
--gcs-max-retries  -gcs-retries	20	If the GCS bucket channel errors out, how many times it will attempt to re-initiate the connection
--help  -h	false	display the help message
--imprecise-variant-evidence-threshold	7	Number of pieces of imprecise evidence necessary to call a variant in the absence of an assembled breakpoint.
--interval-merging-rule  -imr	ALL	Interval merging rule for abutting intervals
--intervals  -L	[]	One or more genomic intervals over which to operate
--max-callable-imprecise-deletion-size	15000	Maximum size deletion to call based on imprecise evidence without corroborating read depth evidence
--min-align-length	50	Minimum flanking alignment length
--non-canonical-contig-names-file  -alt-tigs	null	file containing non-canonical chromosome names (e.g chrUn_KI270588v1) in the reference, human reference (hg19 or hg38) assumed when omitted
--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
--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.
--truth-interval-padding	50	Breakpoint padding for evaluation against truth data.
--version	false	display the version number for this tool
--write-sam	false	output query-name sorted SAM files for local assembly contigs whose alignment signature could not be used for emitting un-ambiguous calls
Optional Common Arguments
--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	[]	Undocumented option
--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
--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.

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--arguments_file / NA

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

List[File]  []

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--assembly-imprecise-evidence-overlap-uncertainty / NA

Uncertainty in overlap of assembled breakpoints and evidence target links.

int  100  [ [ -∞  ∞ ] ]

---

--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  [ [ -∞  ∞ ] ]

---

--cnv-calls / NA

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

String  null

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--conf / -conf

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

List[String]  []

---

--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]  []

---

--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  [ [ -∞  ∞ ] ]

---

--help / -h

display the help message

boolean  false

---

--imprecise-variant-evidence-threshold / NA

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

int  7  [ [ -∞  ∞ ] ]

---

--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

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--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]  []

---

--max-callable-imprecise-deletion-size / NA

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

int  15000  [ [ -∞  ∞ ] ]

---

--min-align-length / NA

Minimum flanking alignment length

Integer  50  [ [ -∞  ∞ ] ]

---

--non-canonical-contig-names-file / -alt-tigs

file containing non-canonical chromosome names (e.g chrUn_KI270588v1) in the reference, human reference (hg19 or hg38) assumed when omitted

String  null

---

--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

prefix for output files (including VCF files and if enabled, the signaling assembly contig's alignments); sample name will be appended after the provided argument

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

---

--program-name / NA

Name of the program running

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-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

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--reference / -R

Reference sequence file

R String  null

---

--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[*]

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--TMP_DIR / NA

Undocumented option

List[File]  []

---

--truth-interval-padding / NA

Breakpoint padding for evaluation against truth data.

int  50  [ [ -∞  ∞ ] ]

---

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

Whether to use the JdkDeflater (as opposed to IntelDeflater)

boolean  false

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

Whether to use the JdkInflater (as opposed to IntelInflater)

boolean  false

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--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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--version / NA

display the version number for this tool

boolean  false

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--write-sam / NA

output query-name sorted SAM files for local assembly contigs whose alignment signature could not be used for emitting un-ambiguous calls

boolean  false

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GATK version 4.0.5.2 built at 25-50-2019 01:50:01.