BwaMemIndexImageCreator

Create a BWA-MEM index image file for use with GATK BWA tools

Category Reference

Overview

Create a BWA-MEM index image file for use with GATK BWA tools

Tools that utilize BWA-MEM (e.g. BwaSpark, PathSeqBwaSpark) require an index image file of the reference sequences. This tool generates the image file from a reference FASTA file.

Input

Reference FASTA file

Output

BWA-MEM index image file of the reference

Usage example

 gatk BwaMemIndexImageCreator \
     -I reference.fasta \
     -O reference.fasta.img

BwaMemIndexImageCreator 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		Input reference FASTA file location.
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
--output -O		Output reference index image file (ending in ".img").
--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] []

--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 ""

--help / -h

display the help message

boolean false

--input / -I

Input reference FASTA file location.

R String null

--output / -O

Output reference index image file (ending in ".img").
If not provided, the default image file path will be the same as the reference FASTA with the extension ".img".

String null