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Nvidia Clara Parabricks genotypegvcf

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Description

This tool converts variant calls in g.vcf format to VCF format.

Publisher

Nvidia

Latest Tag

4.0.0-1

Modified

November 1, 2022

Compressed Size

89.29 MB

Multinode Support

No

Multi-Arch Support

No

4.0.0-1 (Latest) Scan Results

Linux / amd64

This tool applies an accelerated GATK GenotypeGVCFs for joint genotyping, converting from g.vcf format to regular VCF format. This utilizes the HaplotypeCaller genotype likelihoods, produced with the -ERC GVCF flag, to joint genotype on one or more (multi-sample) g.vcf files.

For further information visit the genotypegvcf help page.

Quick Start

# 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:<VERSION-TAG> \
    pbrun genotypegvcf \
    --ref /workdir/${REFERENCE_FILE} \
    --in-gvcf /workdir/${INPUT_GVCF_FILE} \
    --out-vcf /outputdir/${OUTPUT_VCF}