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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
null 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
--help
 -h
false display the help message
--output
 -O
null Output reference index image file (ending in ".img").
--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
[] Undocumented option
--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]  []


--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  [ [ -∞  ∞ ] ]


--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


--QUIET / NA

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

Boolean  false


--showHidden / -showHidden

display hidden arguments

boolean  false


--TMP_DIR / NA

Undocumented option

List[File]  []


--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


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GATK version 4.0.4.0 built at 23-40-2018 11:40:56.