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
GATK version 4.1.1.0 built at Sat, 23 Nov 2019 17:29:19 -0500.
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