(Internal) Examines aligned contigs from local assemblies and calls structural variants or their breakpoints
Category Structural Variant Discovery
Overview
(Internal) Examines aligned contigs from local assemblies and calls structural variants or their breakpointsThis 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 | |
--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 | |
--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 | |
--min-mq -mq |
30 | Minimum mapping quality of evidence assembly contig | |
--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 | |||
--add-output-vcf-command-line |
true | If true, adds a command line header line to created VCF files. | |
--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 | |||
--debug-mode |
false | Run interpretation tool in debug mode (more information print to screen) | |
--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-vcf-command-line / -add-output-vcf-command-line
If true, adds a command line header line to created VCF files.
boolean true
--arguments_file / NA
read one or more arguments files and add them to the command line
List[File] []
--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
--conf / -conf
spark properties to set on the spark context in the format =
List[String] []
--debug-mode / NA
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).
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 [ [ -∞ ∞ ] ]
--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
--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
--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 [ [ -∞ ∞ ] ]
--min-mq / -mq
Minimum mapping quality of evidence assembly contig
Integer 30 [ [ -∞ ∞ ] ]
--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
--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[*]
--tmp-dir / NA
Temp directory to use.
String null
--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
--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-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
GATK version 4.0.12.0 built at 25-04-2019 03:04:01.
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