genotypegvcf

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

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.

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 \
    --workdir /workdir \
    nvcr.io/nvidia/clara/clara-parabricks:4.2.1-1 \
    pbrun genotypegvcf \
    --ref /workdir/${REFERENCE_FILE} \
    --in-gvcf /workdir/${INPUT_GVCF_FILE} \
    --out-vcf /outputdir/${OUTPUT_VCF}

Compatible CPU GATK4 Command

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            $ gatk GenotypeGVCFs \
    -R <INPUT_DIR>/${REFERENCE_FILE} \
    -V <INPUT_DIR>/${INPUT_GVCF_FILE} \
    -O <OUTPUT_DIR>/${OUTPUT_VCF}

genotypegvcf Reference

Convert GVCF to VCF.

Input/Output file options

--ref REF
--in-gvcf IN_GVCF
--out-vcf OUT_VCF

Options specific to this tool

(none)

Performance Options:

--num-threads NUM_THREADS

Common options:

--logfile LOGFILE
--tmp-dir TMP_DIR
--with-petagene-dir WITH_PETAGENE_DIR
--keep-tmp
--no-seccomp-override
--version