SortSam (Picard)

This tool sorts the input SAM or BAM file by coordinate, queryname (QNAME), or some other property of the SAM record. The SortOrder of a SAM/BAM file is found in the SAM file header tag @HD in the field labeled SO.

For a coordinate sorted SAM/BAM file, read alignments are sorted first by the reference sequence name (RNAME) field using the reference sequence dictionary (@SQ tag). Alignments within these subgroups are secondarily sorted using the left-most mapping position of the read (POS). Subsequent to this sorting scheme, alignments are listed arbitrarily.

For queryname-sorted alignments, the tool orders records deterministically by queryname field followed by record strand orientation flag, primary record flag, and secondary alignment flag. This ordering may change in future versions.

Usage example:

java -jar picard.jar SortSam \
      I=input.bam \
      O=sorted.bam \
      SORT_ORDER=coordinate

Category Read Data Manipulation

Overview

Sorts a SAM or BAM file.

Summary

This tool sorts the input SAM or BAM file by coordinate, queryname (QNAME), or some other property of the SAM record. The SortOrder of a SAM/BAM file is found in the SAM file header tag labeled SO.

For a coordinate sorted SAM/BAM file, read alignments are sorted first by the reference sequence name (RNAME) field using the reference sequence dictionary tag labeled SQ. Alignments within these subgroups are secondarily sorted using the left-most mapping position of the read (POS). Subsequent to this sorting scheme, alignments are listed arbitrarily.

Inputs

Input BAM or SAM file to sort
Sorted BAM or SAM output file
Sort order of output file

Usage example:

     java -jar picard.jar SortSam \
     INPUT=input.bam \
     OUTPUT=sorted.bam \
     SORT_ORDER=coordinate

SortSam (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	Input BAM or SAM file to sort.
--OUTPUT -O	null	Sorted BAM or SAM output file.
--SORT_ORDER -SO	null	Sort order of output file.
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
--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

Input BAM or SAM file to sort.

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

Sorted BAM or SAM output file.

R File null

--QUIET / NA

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

Boolean false

--REFERENCE_SEQUENCE / -R

Reference sequence file.

File null

--showHidden / -showHidden

display hidden arguments

boolean false

--SORT_ORDER / -SO

Sort order of output file.

The --SORT_ORDER argument is an enumerated type (SortOrder), which can have one of the following values:

queryname
coordinate
duplicate

R SortOrder null

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