prepon - NVIDIA Docs

Generate an index for a PON file. This is a prerequisite for using the "--pon" option in mutectcaller.

prepon requires that the Contig field be present in the header of the input .vcf.gz file in order to do memory allocation at the start of execution. This field should include both the chromosome name and length:

Copy
Copied!

            
            ##contig=<ID=chr1,length=248956422>
##contig=<ID=chr2,length=242193529>
##contig=<ID=chr3,length=198295559>
...

If your input .vcf.gz file does not include these value, run this command to update the header before running prepon:

Copy
Copied!

            
            $ bcftools reheader --fai YOUR_REFERENCE_FILE.fa.fai INPUT_PON.vcf.gz > UPDATED_PON.vcf.gz

See the prepon Reference section for a detailed listing of all available options.

Quick Start

Copy
Copied!

            
            # 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:4.3.2-1 (OR nvcr.io/nvidia/clara/clara-parabricks:4.3.2-1.grace) \
    pbrun prepon \
    --in-pon-file /workdir/${INPUT_PON_VCF}

prepon Reference

Build the index for a PON file; this is a prerequisite for mutect pon

Input/Output file options

--in-pon-file IN_PON_FILE

Path to the input PON file in vcf.gz format with its tabix index. (default: None)

Option is required.

Options specific to this tool

(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.

GPU options:

--num-gpus NUM_GPUS: Number of GPUs to use for a run. GPUs 0..(NUM_GPUS-1) will be used.