Examines alignments of chimeric contigs, attempting to produce an optimal tiling
Category Diagnostics and Quality Control
Overview(Internal) Examines alignments of chimeric contigs, attempting to produce an optimal tiling
This tool is used in development and should not be of interest to most researchers. It is a prototype of one aspect of structural variant calling from chimeric contigs produced by local assemblies.
It takes a SAM/BAM/CRAM containing the alignments of assembled contigs and filters them with the aim of providing "optimal coverage" of the contig, based on an heuristic scoring scheme.
It saves the result as a text file, formatted as:
- An input file of contigs from local assemblies aligned to reference.
- A text file describing the selected alignments.
gatk FilterLongReadAlignmentsSAMSpark \ -I assemblies.sam \ -O selected_alignments.txt
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.
FilterLongReadAlignmentsSAMSpark 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|
|||BAM/SAM/CRAM file containing reads|
|null||prefix for output text file for filtered alignment intervals|
|Optional Tool Arguments|
||||read one or more arguments files and add them to the command line|
||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).|
||||spark properties to set on the spark context in the format
||false||If specified, do not check the sequence dictionaries from our inputs for compatibility. Use at your own risk!|
|20||If the GCS bucket channel errors out, how many times it will attempt to re-initiate the connection|
|false||display the help message|
|ALL||Interval merging rule for abutting intervals|
|||One or more genomic intervals over which to operate|
|null||file containing non-canonical contig names (e.g chrUn_KI270588v1) in the reference, human reference assumed when omitted|
||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.|
|false||whether to run old way of filtering or not|
||null||Name of the program running|
||false||For tools that write an output, write the output in multiple pieces (shards)|
||local[*]||URL of the Spark Master to submit jobs to when using the Spark pipeline runner.|
||false||display the version number for this tool|
|Optional Common Arguments|
|||Read filters to be disabled before analysis|
||false||Disable all tool default read filters|
|||One or more genomic intervals to exclude from processing|
||null||A configuration file to use with the GATK.|
|0||Amount of padding (in bp) to add to each interval you are excluding.|
|0||Amount of padding (in bp) to add to each interval you are including.|
|UNION||Set merging approach to use for combining interval inputs|
||false||Whether to suppress job-summary info on System.err.|
|||Read filters to be applied before analysis|
||||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.|
|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.|
|false||Whether to use the JdkDeflater (as opposed to IntelDeflater)|
|false||Whether to use the JdkInflater (as opposed to IntelInflater)|
||INFO||Control verbosity of logging.|
|0.0||Maximum difference between alignment configuration scores for which two configurations will be considered equally likely|
||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.
--arguments_file / NA
read one or more arguments files and add them to the command line
--bam-partition-size / NA
long 0 [ [ -∞ ∞ ] ]
--conf / -conf
spark properties to set on the spark context in the format
Maximum difference between alignment configuration scores for which two configurations will be considered equally likely
Double 0.0 [ [ -∞ ∞ ] ]
--disable-read-filter / -DF
Read filters to be disabled before analysis
--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!
--disable-tool-default-read-filters / -disable-tool-default-read-filters
Disable all tool default read filters
--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).
--gatk-config-file / NA
A configuration file to use with the GATK.
--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
--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:
--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:
- Take the union of all intervals
- Take the intersection of intervals (the subset that overlaps all intervals specified)
--intervals / -L
One or more genomic intervals over which to operate
--non-canonical-contig-names-file / -alt-tigs
file containing non-canonical contig names (e.g chrUn_KI270588v1) in the reference, human reference assumed when omitted
--num-reducers / NA
int 0 [ [ -∞ ∞ ] ]
--old-filtering-too / -OT
whether to run old way of filtering or not
--output / -O
prefix for output text file for filtered alignment intervals
R String null
--program-name / NA
Name of the program running
--QUIET / NA
Whether to suppress job-summary info on System.err.
--read-filter / -RF
Read filters to be applied before analysis
--read-index / -read-index
The --read-validation-stringency argument is an enumerated type (ValidationStringency), which can have one of the following values:
--reference / -R
--sharded-output / NA
For tools that write an output, write the output in multiple pieces (shards)
--showHidden / -showHidden
display hidden arguments
--spark-master / NA
URL of the Spark Master to submit jobs to when using the Spark pipeline runner.
--TMP_DIR / NA
--use-jdk-deflater / -jdk-deflater
Whether to use the JdkDeflater (as opposed to IntelDeflater)
--use-jdk-inflater / -jdk-inflater
Whether to use the JdkInflater (as opposed to IntelInflater)
--verbosity / -verbosity
Control verbosity of logging.
The --verbosity argument is an enumerated type (LogLevel), which can have one of the following values:
--version / NA
display the version number for this tool
GATK version 22.214.171.124 built at 27-36-2019 11:36:13.