SplitSamByNumberOfReads (Picard)

Splits a SAM/BAM/CRAM file to multiple files.This tool splits the input query-grouped SAM/BAM/CRAM file into multiple files while maintaining the sort order. This can be used to split a large unmapped input in order to parallelize alignment. It will traverse the input twice unless TOTAL_READS_IN_INPUT is provided. Output type (and extension) will agreewith that of the input.

Usage example:

java -jar picard.jar SplitSamByNumberOfReads \
     I=paired_unmapped_input.bam \
     OUTPUT=out_dir \ 
     TOTAL_READS_IN_INPUT=800000000 \ 
     SPLIT_TO_N_READS=48000000

Category Read Data Manipulation

Overview

Splits the input queryname sorted or query-grouped SAM/BAM/CRAM file and writes it into multiple BAM files, each with an approximately equal number of reads. This will retain the sort order within each output BAM and if the BAMs are concatenated in order (output files are named numerically) the order of the reads will match the original BAM. It will traverse the bam twice unless TOTAL_READS_IN_INPUT is provided.

SplitSamByNumberOfReads (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		Input SAM/BAM/CRAM file to split
--OUTPUT -O		Directory in which to output the split BAM files.
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
--OUT_PREFIX	shard	Output files will be named _N.EXT, where N enumerates the output file and EXT is the same as that of the input.
--SPLIT_TO_N_FILES -N_FILES	0	Split to N files.
--SPLIT_TO_N_READS -N_READS	0	Split to have approximately N reads per output file. The actual number of reads per output file will vary by no more than the number of output files * (the maximum number of reads with the same queryname - 1).
--TOTAL_READS_IN_INPUT -TOTAL_READS	0	Total number of reads in the input file. If this is not provided, the input will be read twice, the first time to get a count of the total reads.
--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

Input SAM/BAM/CRAM file to split

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 [ [ -∞ ∞ ] ]

--OUT_PREFIX / -OUT_PREFIX

Output files will be named _N.EXT, where N enumerates the output file and EXT is the same as that of the input.

String shard

--OUTPUT / -O

Directory in which to output the split BAM files.

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

--SPLIT_TO_N_FILES / -N_FILES

Split to N files.

Exclusion: This argument cannot be used at the same time as SPLIT_TO_N_READS.

int 0 [ [ -∞ ∞ ] ]

--SPLIT_TO_N_READS / -N_READS

Split to have approximately N reads per output file. The actual number of reads per output file will vary by no more than the number of output files * (the maximum number of reads with the same queryname - 1).

Exclusion: This argument cannot be used at the same time as SPLIT_TO_N_FILES.

int 0 [ [ -∞ ∞ ] ]

--TMP_DIR

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

List[File] []

--TOTAL_READS_IN_INPUT / -TOTAL_READS

Total number of reads in the input file. If this is not provided, the input will be read twice, the first time to get a count of the total reads.

long 0 [ [ -∞ ∞ ] ]

--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.