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.
# 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 \
--workdir /workdir \
nvcr.io/nvidia/clara/clara-parabricks:4.2-1 \
pbrun indexgvcf \
--input /workdir/${INPUT_GVCF}
$ gatk IndexFeatureFile -I <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
(none)
Common options:
- --logfile LOGFILE
- --tmp-dir TMP_DIR
- --with-petagene-dir WITH_PETAGENE_DIR
- --keep-tmp
- --no-seccomp-override
- --version
Path to the log file. If not specified, messages will only be written to the standard error output. (default: None)
Full path to the directory where temporary files will be stored.
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.