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.

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 4.0.11.0 built at 23-11-2018 02:11:49.