Nvidia Clara Parabricks genotypegvcf

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}