Merges multiple SAM and/or BAM files into a single file. This tool is used for combining SAM and/or BAM files from different runs or read groups into a single file, similarly to the "merge" function of Samtools (http://www.htslib.org/doc/samtools.html).
Note that to prevent errors in downstream processing, it is critical to identify/label read groups appropriately. If different samples contain identical read group IDs, this tool will avoid collisions by modifying the read group IDs to be unique. For more information about read groups, see the GATK Dictionary entry.
Usage example:
java -jar picard.jar MergeSamFiles \
I=input_1.bam \
I=input_2.bam \
O=output_merged_files.bam
Category Read Data Manipulation
Overview
This tool is used for combining SAM and/or BAM files from different runs or read groups into a single file, similar to the \"merge\" function of Samtools (http://www.htslib.org/doc/samtools.html).Note that to prevent errors in downstream processing, it is critical to identify/label read groups appropriately. If different samples contain identical read group IDs, this tool will avoid collisions by modifying the read group IDs to be unique. For more information about read groups, see the GATK Dictionary entry.
Usage example:
java -jar picard.jar MergeSamFiles \\
I=input_1.bam \\
I=input_2.bam \\
O=output_merged_files.bam
MergeSamFiles (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 |
SAM or BAM input file | ||
--OUTPUT -O |
SAM or BAM file to write merged result to | ||
Optional Tool Arguments | |||
--arguments_file |
read one or more arguments files and add them to the command line | ||
--ASSUME_SORTED -AS |
false | If true, assume that the input files are in the same sort order as the requested output sort order, even if their headers say otherwise. | |
--COMMENT -CO |
Comment(s) to include in the merged output file's header. | ||
--help -h |
false | display the help message | |
--INTERVALS -RGN |
An interval list file that contains the locations of the positions to merge. Assume bam are sorted and indexed. The resulting file will contain alignments that may overlap with genomic regions outside the requested region. Unmapped reads are discarded. | ||
--MERGE_SEQUENCE_DICTIONARIES -MSD |
false | Merge the sequence dictionaries | |
--SORT_ORDER -SO |
coordinate | Sort order of output file | |
--USE_THREADING |
false | Option to create a background thread to encode, compress and write to disk the output file. The threaded version uses about 20% more CPU and decreases runtime by ~20% when writing out a compressed BAM file. | |
--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 |
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] []
--ASSUME_SORTED / -AS
If true, assume that the input files are in the same sort order as the requested output sort order, even if their headers say otherwise.
boolean false
--COMMENT / -CO
Comment(s) to include in the merged output file's header.
List[String] []
--COMPRESSION_LEVEL
Compression level for all compressed files created (e.g. BAM and VCF).
int 5 [ [ -∞ ∞ ] ]
--CREATE_INDEX
Whether to create a BAM index when writing a coordinate-sorted BAM file.
Boolean false
--CREATE_MD5_FILE
Whether to create an MD5 digest for any BAM or FASTQ files created.
boolean false
--GA4GH_CLIENT_SECRETS
Google Genomics API client_secrets.json file path.
String client_secrets.json
--help / -h
display the help message
boolean false
--INPUT / -I
SAM or BAM input file
R List[String] []
--INTERVALS / -RGN
An interval list file that contains the locations of the positions to merge. Assume bam are sorted and indexed. The resulting file will contain alignments that may overlap with genomic regions outside the requested region. Unmapped reads are discarded.
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 [ [ -∞ ∞ ] ]
--MERGE_SEQUENCE_DICTIONARIES / -MSD
Merge the sequence dictionaries
boolean false
--OUTPUT / -O
SAM or BAM file to write merged result to
R File null
--QUIET
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:
- unsorted
- queryname
- coordinate
- duplicate
- unknown
SortOrder coordinate
--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
--USE_THREADING
Option to create a background thread to encode, compress and write to disk the output file. The threaded version uses about 20% more CPU and decreases runtime by ~20% when writing out a compressed BAM file.
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
GATK version 4.1.8.0-SNAPSHOT built at Tue, 30 Jun 2020 17:28:31 -0400.
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