Showing tool doc from version 4.0.4.0 | The latest version is 4.1.3.0

**BETA** CreateHadoopBamSplittingIndex

Create a Hadoop BAM splitting index

Category Other


Overview

Create a Hadoop BAM splitting index and optionally a BAM index from a BAM file.

Input

  • A BAM file

Output

  • BAM splitting index file
  • BAM bai index (optional)

Usage example

     gatk CreateHadoopBamSplittingIndex \
         -I input_reads.bam \
         -O input_reads.bam.splitting-bai
 

CreateHadoopBamSplittingIndex 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 BAM file to create a HadoopBam splitting index for
Optional Tool Arguments
--arguments_file
[] read one or more arguments files and add them to the command line
--create-bai
false Set this to create a bai index at the same time as creating a splitting index
--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 The BAM splitting_index file. If this is unspecified an index will be created with the same name as the input file but with the additional extension .splitting-bai
--splitting-index-granularity
4096 Splitting index granularity, an entry is created in the index every this many reads.
--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.
--read-validation-stringency
 -VS
SILENT Validation stringency for all SAM/BAM/CRAM/SRA files read by this program. The default stringency value SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded.
--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]  []


--create-bai / NA

Set this to create a bai index at the same time as creating a splitting index

boolean  false


--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

BAM file to create a HadoopBam splitting index for

R File  null


--output / -O

The BAM splitting_index file. If this is unspecified an index will be created with the same name as the input file but with the additional extension .splitting-bai

File  null


--QUIET / NA

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

Boolean  false


--read-validation-stringency / -VS

Validation stringency for all SAM/BAM/CRAM/SRA files read by this program. The default stringency value 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 --read-validation-stringency argument is an enumerated type (ValidationStringency), which can have one of the following values:

STRICT
LENIENT
SILENT

ValidationStringency  SILENT


--showHidden / -showHidden

display hidden arguments

boolean  false


--splitting-index-granularity / NA

Splitting index granularity, an entry is created in the index every this many reads.

int  4096  [ [ -∞  ∞ ] ]


--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


Return to top


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

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