prepon

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:

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##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:

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

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# 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:4.2.1-1 \ pbrun prepon \ --in-pon-file /workdir/${INPUT_PON_VCF}

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.

© Copyright 2023, Nvidia. Last updated on Dec 13, 2023.