Very simple command that just reads a SAM or BAM file andwrites out the header and each record to standard out. When an (optional) intervalsfile is specified, only records overlapping those intervals will be output. All reads, just the aligned reads, or just the unaligned reads can be printed out bysetting AlignmentStatus accordingly. The SAM or BAM header can be printed out separatelyusing HEADER_ONLY. Only the alignment records can be printed using RECORDS_ONLY.However, HEADER_ONLY and RECORDS_ONLY cannot both be specified at one time.
Usage example:
java -jar picard.jar ViewSam
I=sample.bam
HEADER_ONLY=true
Category Diagnostics and Quality Control
Overview
Prints a SAM or BAM file to the screen.Very simple command that just reads a SAM or BAM file and writes out the header and each record to standard out. When an (optional) intervals file is specified, only records overlapping those intervals will be output.
All reads, just the aligned reads, or just the unaligned reads can be printed out by setting AlignmentStatus accordingly. The SAM or BAM header can be printed out separately using HEADER_ONLY. Only the alignment records can be printed using RECORDS_ONLY. However, HEADER_ONLY and RECORDS_ONLY cannot both be specified at one time.
Inputs
- A SAM or BAM file to be viewed
- Optional arguments specifying which reads or records need to be viewed
Usage example:
java -jar picard.jar ViewSam \ I=input_reads.bam \ HEADER_ONLY=true
ViewSam (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 | The SAM or BAM file or GA4GH url to view. | |
Optional Tool Arguments | |||
--ALIGNMENT_STATUS |
All | Print out all reads, just the aligned reads or just the unaligned reads. | |
--arguments_file |
[] | read one or more arguments files and add them to the command line | |
--HEADER_ONLY |
false | Print the SAM header only. | |
--help -h |
false | display the help message | |
--INTERVAL_LIST |
null | An intervals file used to restrict what records are output. | |
--PF_STATUS |
All | Print out all reads, just the PF reads or just the non-PF reads. | |
--RECORDS_ONLY |
false | Print the alignment records only. | |
--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.
--ALIGNMENT_STATUS / NA
Print out all reads, just the aligned reads or just the unaligned reads.
The --ALIGNMENT_STATUS argument is an enumerated type (AlignmentStatus), which can have one of the following values:
- Aligned
- Unaligned
- All
AlignmentStatus All
--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
--HEADER_ONLY / NA
Print the SAM header only.
boolean false
--help / -h
display the help message
boolean false
--INPUT / -I
The SAM or BAM file or GA4GH url to view.
R String null
--INTERVAL_LIST / NA
An intervals file used to restrict what records are output.
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 [ [ -∞ ∞ ] ]
--PF_STATUS / NA
Print out all reads, just the PF reads or just the non-PF reads.
The --PF_STATUS argument is an enumerated type (PfStatus), which can have one of the following values:
- PF
- NonPF
- All
PfStatus All
--QUIET / NA
Whether to suppress job-summary info on System.err.
Boolean false
--RECORDS_ONLY / NA
Print the alignment records only.
boolean false
--REFERENCE_SEQUENCE / -R
Reference sequence file.
File null
--showHidden / -showHidden
display hidden arguments
boolean false
--TMP_DIR / NA
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
--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 4.0.0.0 built at 27-36-2019 11:36:13.
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