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ViewSam (Picard)

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


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GATK version 4.0.3.0 built at 09-43-2018 09:43:10.