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

 # 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 \ \
    pbrun indexgvcf \
    --input /workdir/${INPUT_GVCF}

Compatible CPU GATK4 Command

$ 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.

Options specific to this tool


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)


Do not delete the directory storing temporary files after completion.


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


View compatible software versions.