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:

##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:

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

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

Quick Start

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# This command assumes all the inputs are in the current working directory and all the outputs go to the same place.
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docker run --rm --gpus all --volume $(pwd):/workdir --volume $(pwd):/outputdir \
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    --workdir /workdir \
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    nvcr.io/nvidia/clara/clara-parabricks:4.7.1-1 \
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    pbrun prepon \
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    --in-pon-file /workdir/${INPUT_PON_VCF}

Options