# 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


## Quick Start

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# This command assumes all the inputs are in <INPUT_DIR> and all the outputs go to <OUTPUT_DIR>.
$docker run --rm --gpus all --volume <INPUT_DIR>:/workdir --volume <OUTPUT_DIR>:/outputdir -w /workdir \ nvcr.io/nvidia/clara/clara-parabricks:v4.0.1-1 \ pbrun prepon \ --in-pon-file /workdir/${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.

(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.