genotypegvcf - NVIDIA Docs

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

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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
    -w /workdir \
    nvcr.io/nvidia/clara/clara-parabricks:v4.0.1-1 \
    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

Path to the reference file. (default: None)

Option is required.

--in-gvcf IN_GVCF

Input a g.vcf or g.vcf.gz file that will be converted to VCF. Required if --in-selectvariants-dir is not specified. (default: None)

--in-selectvariants-dir IN_SELECTVARIANTS_DIR

Path to output directory of selectvariants. (default: None)

--out-vcf OUT_VCF

Path to output VCF file. (default: None)

Option is required.

Tool Options:

--num-threads NUM_THREADS: Number of threads for worker. (default: 4)

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.