Creates an index for a feature file, e.g. VCF or BED file.
Category Other
Overview
This tool creates an index file for the various kinds of feature-containing files supported by GATK (such as VCF and BED files). An index allows querying features by a genomic interval.Usage example
gatk IndexFeatureFile \
-F cohort.vcf.gz
This produces the corresponding index, cohort.vcf.gz.tbi.
IndexFeatureFile 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 | |||
|
--feature-file -F |
null | Feature file (eg., VCF or BED file) to index. Must be in a tribble-supported format | |
| 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 | The output index file. If missing, the tool will create an index file in the same directory as the input file. | |
|
--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] []
--feature-file / -F
Feature file (eg., VCF or BED file) to index. Must be in a tribble-supported format
R File null
--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
--output / -O
The output index file. If missing, the tool will create an index file in the same directory as the input file.
File 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
GATK version 4.0.1.2 built at 02-02-2019 02:02:55.
2 comments
This documentation is wrong for version 4.2.5:
--input,-I <GATKPath> Feature file (eg., VCF or BED file) to index. Must be in a tribble-supported format
Required.
Why would you change your argument for a minor revision/release?
Please update for GATK 4.3
"A USER ERROR has occurred: feature-file is not a recognized option"
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