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SplitSamByNumberOfReads (Picard)

Splits a SAM or BAM file to multiple BAMs.This tool splits the input query-grouped SAM/BAM file into multiple BAM files while maintaining the sort order. This can be used to split a large unmapped BAM in order to parallelize alignment. It will traverse the bam twice unless TOTAL_READS_IN_INPUT is provided.

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 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
null Input SAM/BAM file to split
--OUTPUT
 -O
null 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.bam, where N enumerates the output file.
--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 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 SAM/BAM file to split

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  [ [ -∞  ∞ ] ]


--OUT_PREFIX / -OUT_PREFIX

Output files will be named _N.bam, where N enumerates the output file.

String  shard


--OUTPUT / -O

Directory in which to output the split BAM files.

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


--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, N_FILES.

int  0  [ [ -∞  ∞ ] ]


--TMP_DIR / NA

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 / 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 4.1.1.0 built at Wed, 3 Apr 2019 09:19:24 -0400.