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.
See the indexgvcf Reference section for a detailed listing of all available options.
# This command assumes all the inputs are in the current working directory and all the outputs go to the same place.
docker run --rm --gpus all --volume $(pwd):/workdir --volume $(pwd):/outputdir \
--workdir /workdir \
nvcr.io/nvidia/clara/clara-parabricks:4.5.1-1 \
pbrun indexgvcf \
--input /workdir/${INPUT_GVCF}
$ gatk IndexFeatureFile -I <INPUT_DIR>/${INPUT_GVCF}
Index a GVCF file.
Type | Name | Required? | Description |
|---|---|---|---|
| I/O | ‑‑input INPUT | Yes | Path to the g.vcf/g.vcf.gz file to be indexed. |
| Runtime | ‑‑verbose | No | Enable verbose output. |
| Runtime | ‑‑x3 | No | Show full command line arguments. |
| Runtime | ‑‑logfile LOGFILE | No | Path to the log file. If not specified, messages will only be written to the standard error output. |
| Runtime | ‑‑tmp‑dir TMP_DIR | No | Full path to the directory where temporary files will be stored. (default: .) |
| Runtime | ‑‑with‑petagene‑dir WITH_PETAGENE_DIR | No | 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. Optionally set the PetaLinkMode environment variable that is used to further configure PetaLink, notably setting it to "+write" to enable outputting compressed BAM and .fastq files. |
| Runtime | ‑‑keep‑tmp | No | Do not delete the directory storing temporary files after completion. |
| Runtime | ‑‑no‑seccomp‑override | No | Do not override seccomp options for docker. |
| Runtime | ‑‑version | No | View compatible software versions. |