MergeSamFiles

Merges multiple SAM/BAM files into one file

Category SAM/BAM/CRAM Tools


Overview

Reads a SAM/BAM/CRAM file and combines the output to one file

MergeSamFiles 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/BAM input file
--output
 -O
null SAM/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.
--gcs_max_retries
 -gcs_retries
20 If the GCS bucket channel errors out, how many times it will attempt to re-initiate the connection
--help
 -h
false display the help message
--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 GELI).
--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.
--MAX_RECORDS_IN_RAM
500000 When writing SAM 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 a SAM file, and increases the amount of RAM needed.
--QUIET
false Whether to suppress job-summary info on System.err.
--reference
 -R
null Reference sequence file.
--TMP_DIR
[] Undocumented option
--use_jdk_deflater
 -jdk_deflater
false Whether to use the JdkDeflater (as opposed to IntelDeflater)
--use_jdk_inflater
 -jdk_inflater
false Whether to use the JdkInflater (as opposed to IntelInflater)
--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]  []


--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 / NA

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

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


--gcs_max_retries / -gcs_retries

If the GCS bucket channel errors out, how many times it will attempt to re-initiate the connection

int  20  [ [ -∞  ∞ ] ]


--help / -h

display the help message

boolean  false


--input / -I

SAM/BAM input file

R List[File]  []


--MAX_RECORDS_IN_RAM / NA

When writing SAM 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 a SAM file, and increases the amount of RAM needed.

Integer  500000  [ [ -∞  ∞ ] ]


--MERGE_SEQUENCE_DICTIONARIES / -MSD

Merge the sequence dictionaries

boolean  false


--output / -O

SAM/BAM file to write merged result to

R File  null


--QUIET / NA

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

Boolean  false


--reference / -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 / NA

Undocumented option

List[File]  []


--use_jdk_deflater / -jdk_deflater

Whether to use the JdkDeflater (as opposed to IntelDeflater)

boolean  false


--use_jdk_inflater / -jdk_inflater

Whether to use the JdkInflater (as opposed to IntelInflater)

boolean  false


--USE_THREADING / NA

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 / 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 / -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 / NA

display the version number for this tool

boolean  false


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GATK version 4.beta.5-SNAPSHOT built at 13-45-2017 04:45:04.