Showing tool doc from version 4.1.3.0 | The latest version is 4.1.3.0

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


Return to top


See also General Documentation | Tool Docs Index Tool Documentation Index | Support Forum

GATK version 4.1.3.0 built at Fri, 9 Aug 2019 21:16:03 -0400.