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/CRAM file is found in the SAM file header tag @HD in the field labeled SO.

For a coordinate sorted SAM/BAM/CRAM 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

@author alecw@broadinstitute.org

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		The SAM, BAM or CRAM file to sort.
--OUTPUT -O		The sorted SAM, BAM or CRAM output file.
--SORT_ORDER -SO		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 an index when writing VCF or coordinate sorted BAM output.
--CREATE_MD5_FILE	false	Whether to create an MD5 digest for any BAM or FASTQ files created.
--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		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

read one or more arguments files and add them to the command line

List[File] []

--COMPRESSION_LEVEL

Compression level for all compressed files created (e.g. BAM and VCF).

int 5 [ [ -∞ ∞ ] ]

--CREATE_INDEX

Whether to create an index when writing VCF or coordinate sorted BAM output.

Boolean false

--CREATE_MD5_FILE

Whether to create an MD5 digest for any BAM or FASTQ files created.

boolean false

--help / -h

display the help message

boolean false

--INPUT / -I

The SAM, BAM or CRAM file to sort.

R File null

--MAX_RECORDS_IN_RAM

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 sorted SAM, BAM or CRAM output file.

R File null

--QUIET

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

Boolean false

--REFERENCE_SEQUENCE / -R

Reference sequence file.

PicardHtsPath 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: Sorts according to the readname. This will place read-pairs and other derived reads (secondary and supplementary) adjacent to each other. Note that the readnames are compared lexicographically, even though they may include numbers. In paired reads, Read1 sorts before Read2.
coordinate: Sorts primarily according to the SEQ and POS fields of the record. The sequence will sorted according to the order in the sequence dictionary, taken from from the header of the file. Within each reference sequence, the reads are sorted by the position. Unmapped reads whose mates are mapped will be placed near their mates. Unmapped read-pairs are placed after all the mapped reads and their mates.
duplicate: Sorts the reads so that duplicates reads are adjacent. Required that the mate-cigar (MC) tag is present. The resulting will be sorted by library, unclipped 5-prime position, orientation, and mate's unclipped 5-prime position.

R SortOrder null

--TMP_DIR

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

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

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

display the version number for this tool

boolean false

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GATK version 4.6.2.0 built at Sun, 13 Apr 2025 13:21:43 -0400.