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		Headerless Hadoop BAM shard to be converted into a readable BAM
--bam-with-header		Well-formed BAM whose header to use for the converted fragment
--output -O		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. User must have storage.buckets.get permission on the bucket being accessed.
--help -h	false	display the help message
--version	false	display the version number for this tool
Optional Common Arguments
--gatk-config-file		A configuration file to use with the GATK.
--QUIET	false	Whether to suppress job-summary info on System.err.
--tmp-dir		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

read one or more arguments files and add them to the command line

List[File] []

--bam-shard

Headerless Hadoop BAM shard to be converted into a readable BAM

R File null

--bam-with-header

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

R File null

--gatk-config-file

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

Project to bill when accessing "requester pays" buckets. If unset, these buckets cannot be accessed. User must have storage.buckets.get permission on the bucket being accessed.

String ""