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.sbior 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 |
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. User must have storage.buckets.get permission on the bucket being accessed. | ||
--help -h |
false | display the help message | |
--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 | ||
--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 |
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 |
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] []
--create-bai
Set this to create a bai index at the same time as creating a splitting index
boolean false
--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
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
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
Splitting index granularity, an entry is created in the index every this many reads.
long 4096 [ [ -∞ ∞ ] ]
--tmp-dir
Temp directory to use.
GATKPath 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
display the version number for this tool
boolean false
GATK version 4.2.4.0-SNAPSHOT built at Thu, 16 Dec 2021 11:57:48 -0800.
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