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.sbi
 

or if one wants to generate bai as well

     gatk CreateHadoopBamSplittingIndex \
         -I input_reads.bam \
         -O input_reads.bam.sbi \
         --create-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
--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
--output  -O	null	The splitting index (SBI) file. If this is unspecified an index will be created with the same name as the input file but with the additional extension .sbi
--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	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]  []

---

--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  [ [ -∞  ∞ ] ]

---

--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

---

--input / -I

BAM file to create a HadoopBam splitting index for

R File  null

---

--output / -O

The splitting index (SBI) file. If this is unspecified an index will be created with the same name as the input file but with the additional extension .sbi

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.

long  4096  [ [ -∞  ∞ ] ]

---

--tmp-dir / NA

Temp directory to use.

GATKPathSpecifier  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

---

GATK version 4.1.3.0 built at Sat, 23 Nov 2019 16:20:54 -0500.