Writes an interval list created by splitting a reference at Ns.A Program for breaking up a reference into intervals of alternating regions of N and ACGT bases.
Used for creating a broken-up interval list that can be used for scattering a variant-calling pipeline in a way that will not cause problems at the edges of the intervals. By using large enough N blocks (so that the tools will not be able to anchor on both sides) we can be assured that the results of scattering and gathering the variants with the resulting interval list will be the same as calling with one large region.
Input
- A reference file to use for creating the intervals (needs to have index and dictionary next to it.) - Which type of intervals to emit in the output (Ns only, ACGT only or both.) - An integer indicating the largest number of Ns in a contiguous block that will be "tolerated" and not converted into an N block.Output
- An interval list (with a SAM header) where the names of the intervals are labeled (either N-block or ACGT-block) to indicate what type of block they define.Usage example
Create an interval list of intervals that do not contain any N blocks for use with haplotype caller on short reads
java -jar picard.jar ScatterIntervalsByNs \ REFERENCE=reference_sequence.fasta \ OUTPUT_TYPE=ACGT \ OUTPUT=output.interval_list
Category Reference
Overview
A Tool for breaking up a reference into intervals of alternating regions of N and ACGT bases.Summary
Used for creating a broken-up interval list that can be used for scattering a variant-calling pipeline in a way that will not cause problems at the edges of the intervals. By using large enough N blocks (so that the tools will not be able to anchor on both sides) we can be assured that the results of scattering and gathering the variants with the resulting interval list will be the same as calling with one large region.Input
Output
An interval list (with a SAM header) where the names of the intervals are labeled (either N-block or ACGT-block) to indicate what type of block they define.
Usage example
Create an interval list of intervals that do not contain any N blocks for use with haplotype caller on short reads
java -jar picard.jar ScatterIntervalsByNs \ R=reference_sequence.fasta \ OT=BOTH \ O=output.interval_list
ScatterIntervalsByNs (Picard) 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 | |||
--OUTPUT -O |
null | Output file for interval list. | |
--REFERENCE -R |
null | Reference sequence to use. Note: this tool requires that the reference fasta has both an associated index and a dictionary. | |
Optional Tool Arguments | |||
--arguments_file |
[] | read one or more arguments files and add them to the command line | |
--help -h |
false | display the help message | |
--MAX_TO_MERGE -N |
1 | Maximal number of contiguous N bases to tolerate, thereby continuing the current ACGT interval. | |
--OUTPUT_TYPE -OT |
BOTH | Type of intervals to output. | |
--version |
false | display the version number for this tool | |
Optional Common Arguments | |||
--COMPRESSION_LEVEL |
5 | Compression level for all compressed files created (e.g. BAM and VCF). | |
--CREATE_INDEX |
false | Whether to create a BAM index when writing a coordinate-sorted BAM file. | |
--CREATE_MD5_FILE |
false | Whether to create an MD5 digest for any BAM or FASTQ files created. | |
--GA4GH_CLIENT_SECRETS |
client_secrets.json | Google Genomics API client_secrets.json file path. | |
--MAX_RECORDS_IN_RAM |
500000 | When writing files that need to be sorted, this will specify the number of records stored in RAM before spilling to disk. Increasing this number reduces the number of file handles needed to sort the file, and increases the amount of RAM needed. | |
--QUIET |
false | Whether to suppress job-summary info on System.err. | |
--TMP_DIR |
[] | One or more directories with space available to be used by this program for temporary storage of working files | |
--USE_JDK_DEFLATER -use_jdk_deflater |
false | Use the JDK Deflater instead of the Intel Deflater for writing compressed output | |
--USE_JDK_INFLATER -use_jdk_inflater |
false | Use the JDK Inflater instead of the Intel Inflater for reading compressed input | |
--VALIDATION_STRINGENCY |
STRICT | Validation stringency for all SAM files read by this program. Setting stringency to SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded. | |
--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.
--arguments_file / NA
read one or more arguments files and add them to the command line
List[File] []
--COMPRESSION_LEVEL / NA
Compression level for all compressed files created (e.g. BAM and VCF).
int 5 [ [ -∞ ∞ ] ]
--CREATE_INDEX / NA
Whether to create a BAM index when writing a coordinate-sorted BAM file.
Boolean false
--CREATE_MD5_FILE / NA
Whether to create an MD5 digest for any BAM or FASTQ files created.
boolean false
--GA4GH_CLIENT_SECRETS / NA
Google Genomics API client_secrets.json file path.
String client_secrets.json
--help / -h
display the help message
boolean false
--MAX_RECORDS_IN_RAM / NA
When writing files that need to be sorted, this will specify the number of records stored in RAM before spilling to disk. Increasing this number reduces the number of file handles needed to sort the file, and increases the amount of RAM needed.
Integer 500000 [ [ -∞ ∞ ] ]
--MAX_TO_MERGE / -N
Maximal number of contiguous N bases to tolerate, thereby continuing the current ACGT interval.
int 1 [ [ -∞ ∞ ] ]
--OUTPUT / -O
Output file for interval list.
R File null
--OUTPUT_TYPE / -OT
Type of intervals to output.
The --OUTPUT_TYPE argument is an enumerated type (OutputType), which can have one of the following values:
- N
- ACGT
- BOTH
OutputType BOTH
--QUIET / NA
Whether to suppress job-summary info on System.err.
Boolean false
--REFERENCE / -R
Reference sequence to use. Note: this tool requires that the reference fasta has both an associated index and a dictionary.
R File null
--showHidden / -showHidden
display hidden arguments
boolean false
--TMP_DIR / NA
One or more directories with space available to be used by this program for temporary storage of working files
List[File] []
--USE_JDK_DEFLATER / -use_jdk_deflater
Use the JDK Deflater instead of the Intel Deflater for writing compressed output
Boolean false
--USE_JDK_INFLATER / -use_jdk_inflater
Use the JDK Inflater instead of the Intel Inflater for reading compressed input
Boolean false
--VALIDATION_STRINGENCY / NA
Validation stringency for all SAM files read by this program. Setting stringency to 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 --VALIDATION_STRINGENCY argument is an enumerated type (ValidationStringency), which can have one of the following values:
- STRICT
- LENIENT
- SILENT
ValidationStringency STRICT
--VERBOSITY / NA
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
GATK version 4.0.5.0 built at 25-10-2019 02:10:54.
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