# indexgvcf

This tool creates an index for g.vcf/g.vcf.gz files. The index file name is determined by appending .tbi to the name of the GVCF file being indexed, and is created in the same directory as the index file itself.

## Quick Start

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# This command assumes all the inputs are in <INPUT_DIR> and all the outputs go to <OUTPUT_DIR>.
$docker run --rm --gpus all --volume <INPUT_DIR>:/workdir --volume <OUTPUT_DIR>:/outputdir -w /workdir \ nvcr.io/nvidia/clara/clara-parabricks:v4.0.1-1 \ pbrun indexgvcf \ --input /workdir/${INPUT_GVCF}


## Compatible CPU GATK4 Command

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$gatk IndexFeatureFile -F <INPUT_DIR>/${INPUT_GVCF}


## indexgvcf Reference

Index a GVCF file.

### Input/Output file options

--input INPUT

Path to the g.vcf/g.vcf.gz file to be indexed.

(default: None)

Option is required.

(none)

### Common options:

--logfile LOGFILE

Path to the log file. If not specified, messages will only be written to the standard error output. (default: None)

--tmp-dir TMP_DIR

Full path to the directory where temporary files will be stored.

--with-petagene-dir WITH_PETAGENE_DIR

Full path to the PetaGene installation directory. By default, this should have been installed at /opt/petagene. Use of this option also requires that the PetaLink library has been preloaded by setting the LD_PRELOAD environment variable. Optionally set the PETASUITE_REFPATH and PGCLOUD_CREDPATH environment variables that are used for data and credentials (default: None)

--keep-tmp

Do not delete the directory storing temporary files after completion.

--no-seccomp-override

Do not override seccomp options for docker (default: None).

--version

View compatible software versions.