BedToIntervalList (Picard)

Converts a BED file to a Picard Interval List. This tool provides easy conversion from BED to the Picard interval_list format which is required by many Picard processing tools. Note that the coordinate system of BED files is such that the first base or position in a sequence is numbered "0", while in interval_list files it is numbered "1".

BED files contain sequence data displayed in a flexible format that includes nine optional fields, in addition to three required fields within the annotation tracks. The required fields of a BED file include:

     chrom - The name of the chromosome (e.g. chr20) or scaffold (e.g. scaffold10671) 
     chromStart - The starting position of the feature in the chromosome or scaffold. The first base in a chromosome is numbered "0" 
     chromEnd - The ending position of the feature in the chromosome or scaffold.  The chromEnd base is not included in the display of the feature. For example, the first 100 bases of a chromosome are defined as chromStart=0, chromEnd=100, and span the bases numbered 0-99.

In each annotation track, the number of fields per line must be consistent throughout a data set. For additional information regarding BED files and the annotation field options, please see: http://genome.ucsc.edu/FAQ/FAQformat.html#format1.

Interval_list files contain sequence data distributed into intervals. The interval_list file format is relatively simple and reflects the SAM alignment format to a degree. A SAM style header must be present in the file that lists the sequence records against which the intervals are described. After the header, the file then contains records, one per line in plain text format with the following values tab-separated::

      -Sequence name (SN) - The name of the sequence in the file for identification purposes, can be chromosome number e.g. chr20 
      -Start position - Interval start position (starts at +1) 
      -End position - Interval end position (1-based, end inclusive) 
      -Strand - Indicates +/- strand for the interval (either + or -) 
      -Interval name - (Each interval should have a unique name)

This tool requires a sequence dictionary, provided with the SEQUENCE_DICTIONARY or SD argument. The value given to this argument can be any of the following:

    - A file with .dict extension generated using Picard's CreateSequenceDictionaryTool
    - A reference.fa or reference.fasta file with a reference.dict in the same directory
    - Another IntervalList with @SQ lines in the header from which to generate a dictionary
    - A VCF that contains #contig lines from which to generate a sequence dictionary
    - A SAM or BAM file with @SQ lines in the header from which to generate a dictionary

Usage example:

java -jar picard.jar BedToIntervalList \
      I=input.bed \
      O=list.interval_list \
      SD=reference_sequence.dict

Category Intervals Manipulation

Overview

BedToIntervalList (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
--INPUT -I	null	The input BED file
--OUTPUT -O	null	The output Picard Interval List
--SEQUENCE_DICTIONARY -SD	null	The sequence dictionary, or BAM/VCF/IntervalList from which a dictionary can be extracted.
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
--SORT	true	If true, sort the output interval list before writing it.
--UNIQUE	false	If true, unique the output interval list by merging overlapping regions, before writing it (implies sort=true).
--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.
--REFERENCE_SEQUENCE -R	null	Reference sequence file.
--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

--INPUT / -I

The input BED file

R File null

--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 [ [ -∞ ∞ ] ]

--OUTPUT / -O

The output Picard Interval List

R File null

--QUIET / NA

Whether to suppress job-summary info on System.err.

Boolean false

--REFERENCE_SEQUENCE / -R

Reference sequence file.

File null

--SEQUENCE_DICTIONARY / -SD

The sequence dictionary, or BAM/VCF/IntervalList from which a dictionary can be extracted.

R File null

--showHidden / -showHidden

display hidden arguments

boolean false

--SORT / NA

If true, sort the output interval list before writing it.

boolean true

--TMP_DIR / NA

One or more directories with space available to be used by this program for temporary storage of working files

List[File] []

--UNIQUE / NA

If true, unique the output interval list by merging overlapping regions, before writing it (implies sort=true).

boolean false

--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.