Showing tool doc from version 4.1.0.0 | The latest version is 4.1.2.0

**BETA** ConvertHeaderlessHadoopBamShardToBam

Convert a headerless BAM shard into a readable BAM

Category Read Data Manipulation


Overview

This is a troubleshooting utility that converts a headerless BAM shard (e.g., a part-r-00000.bam, part-r-00001.bam, etc.), produced by a Spark tool with --sharded-output set to true, into a readable BAM file by adding a header and a BGZF terminator.

This tool is not intended for use with BAM shards that already have a header -- these shards are already readable using samtools.

Input

  • A headerless BAM shard
  • A well-formed BAM whose header will be used for the converted fragment

Output

  • The converted BAM shard

Usage example

 gatk ConvertHeaderlessHadoopBamShardToBam \
     --bam-shard part-r-00000.bam \
     --bam-with-header input.bam \
     -O output.bam
 

ConvertHeaderlessHadoopBamShardToBam 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
--bam-shard
null Headerless Hadoop BAM shard to be converted into a readable BAM
--bam-with-header
null Well-formed BAM whose header to use for the converted fragment
--output
 -O
null Location to write the converted BAM shard
Optional Tool Arguments
--arguments_file
[] read one or more arguments files and add them to the command line
--gcs-max-retries
 -gcs-retries
20 If the GCS bucket channel errors out, how many times it will attempt to re-initiate the connection
--gcs-project-for-requester-pays
"" Project to bill when accessing "requester pays" buckets. If unset, these buckets cannot be accessed.
--help
 -h
false display the help message
--version
false display the version number for this tool
Optional Common Arguments
--gatk-config-file
null A configuration file to use with the GATK.
--QUIET
false Whether to suppress job-summary info on System.err.
--tmp-dir
null Temp directory to use.
--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)
--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]  []


--bam-shard / NA

Headerless Hadoop BAM shard to be converted into a readable BAM

R File  null


--bam-with-header / NA

Well-formed BAM whose header to use for the converted fragment

R File  null


--gatk-config-file / NA

A configuration file to use with the GATK.

String  null


--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  [ [ -∞  ∞ ] ]


--gcs-project-for-requester-pays / NA

Project to bill when accessing "requester pays" buckets. If unset, these buckets cannot be accessed.

String  ""


--help / -h

display the help message

boolean  false


--output / -O

Location to write the converted BAM shard

R File  null


--QUIET / NA

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

Boolean  false


--showHidden / -showHidden

display hidden arguments

boolean  false


--tmp-dir / NA

Temp directory to use.

String  null


--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


--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


Return to top


See also General Documentation | Tool Docs Index Tool Documentation Index | Support Forum

GATK version 4.1.0.0 built at Wed, 30 Jan 2019 10:21:04 +0530.