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.


# 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}


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

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.

© Copyright 2022, Nvidia. Last updated on Feb 22, 2023.