ScatterIntervalsByNs (Picard)

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

A reference file to use for creating the intervals

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 \
       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

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GATK version 4.0.11.0 built at 23-11-2018 02:11:49.