(Internal) Tries to extract simple variants from a provided GATK-SV CPX.vcf
This Read Filter is automatically applied to the data by the Engine before processing by CpxVariantReInterpreterSpark.
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 | |||
| --cpx-vcf |
file containing complex variants as output by GATK-SV | ||
| --input -I |
BAM/SAM/CRAM file containing reads | ||
| --prefix-out-vcf |
prefix for two files containing derived simple variants for complex variants having one/multiple entry in SEGMENT annotation | ||
| --reference -R |
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 |
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. User must have storage.buckets.get permission on the bucket being 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 |
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 |
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 | ||
| --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} | ||
| --truth-interval-padding |
50 | Breakpoint padding for evaluation against truth data. | |
| --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 | |
| 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) | |
| --showHidden |
false | display hidden arguments | |
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.
If true, adds a command line header line to created VCF files.
boolean true
read one or more arguments files and add them to the command line
List[File] []
Uncertainty in overlap of assembled breakpoints and evidence target links.
int 100 [ [ -∞ ∞ ] ]
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 [ [ -∞ ∞ ] ]
External CNV calls file. Should be single sample VCF, and contain only confident autosomal non-reference CNV calls (for now).
String null
Spark properties to set on the Spark context in the format
List[String] []
file containing complex variants as output by GATK-SV
R String null
If true, create a BAM index when writing a coordinate-sorted BAM file.
boolean true
If true, create a BAM splitting index (SBI) when writing a coordinate-sorted BAM file.
boolean true
If true, create a VCF index when writing a coordinate-sorted VCF file.
boolean true
Run interpretation tool in debug mode (more information print to screen)
Boolean false
Read filters to be disabled before analysis
List[String] []
If specified, do not check the sequence dictionaries from our inputs for compatibility. Use at your own risk!
boolean false
Disable all tool default read filters (WARNING: many tools will not function correctly without their default read filters on)
boolean false
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] []
A configuration file to use with the GATK.
String null
If the GCS bucket channel errors out, how many times it will attempt to re-initiate the connection
int 20 [ [ -∞ ∞ ] ]
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 ""
display the help message
boolean false
Number of pieces of imprecise evidence necessary to call a variant in the absence of an assembled breakpoint.
int 7 [ [ -∞ ∞ ] ]
BAM/SAM/CRAM file containing reads
R List[GATKPath] []
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 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:
IntervalMergingRule ALL
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 [ [ -∞ ∞ ] ]
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:
IntervalSetRule UNION
One or more genomic intervals over which to operate
List[String] []
Inverted (with flipped acceptance/failure conditions) read filters applied before analysis (after regular read filters).
List[String] []
Maximum size deletion to call based on imprecise evidence without corroborating read depth evidence
int 15000 [ [ -∞ ∞ ] ]
Minimum flanking alignment length
Integer 50 [ [ -∞ ∞ ] ]
Minimum mapping quality of evidence assembly contig
Integer 30 [ [ -∞ ∞ ] ]
file containing non-canonical chromosome names (e.g chrUn_KI270588v1) in the reference, human reference (hg19 or hg38) assumed when omitted
String null
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 [ [ -∞ ∞ ] ]
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
prefix for two files containing derived simple variants for complex variants having one/multiple entry in SEGMENT annotation
R String null
Name of the program running
String null
Whether to suppress job-summary info on System.err.
Boolean false
Read filters to be applied before analysis
List[String] []
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] []
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:
ValidationStringency SILENT
Reference sequence file
R GATKPath null
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
display hidden arguments
boolean false
URL of the Spark Master to submit jobs to when using the Spark pipeline runner.
String local[*]
Spark verbosity. Overrides --verbosity for Spark-generated logs only. Possible values: {ALL, DEBUG, INFO, WARN, ERROR, FATAL, OFF, TRACE}
String null
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 ∞ ] ]
Temp directory to use.
GATKPath null
Breakpoint padding for evaluation against truth data.
int 50 [ [ -∞ ∞ ] ]
Whether to use the JdkDeflater (as opposed to IntelDeflater)
boolean false
Whether to use the JdkInflater (as opposed to IntelInflater)
boolean false
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
Control verbosity of logging.
The --verbosity argument is an enumerated type (LogLevel), which can have one of the following values:
LogLevel INFO
display the version number for this tool
boolean false
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GATK version 4.6.2.0 built at Sun, 13 Apr 2025 13:21:43 -0400.