Tool ReferenceTools

genotypegvcf

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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.

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

Quick Start

1# This command assumes all the inputs are in the current working directory and all the outputs go to the same place.
2docker run --rm --gpus all --volume $(pwd):/workdir --volume $(pwd):/outputdir \
3    --workdir /workdir \
4    nvcr.io/nvidia/clara/clara-parabricks:4.7.1-1 \
5    pbrun genotypegvcf \
6    --ref /workdir/${REFERENCE_FILE} \
7    --in-gvcf /workdir/${INPUT_GVCF_FILE} \
8    --out-vcf /outputdir/${OUTPUT_VCF}

Compatible CPU GATK4 Command

1$ gatk GenotypeGVCFs \
2    -R <INPUT_DIR>/${REFERENCE_FILE} \
3    -V <INPUT_DIR>/${INPUT_GVCF_FILE} \
4    -O <OUTPUT_DIR>/${OUTPUT_VCF}

Options

TypeNameRequired?Description
I/O--ref REFYesPath to the reference file.
I/O--in-gvcf IN_GVCFYesInput a g.vcf or g.vcf.gz file that will be converted to VCF. Required.
I/O--out-vcf OUT_VCFYesPath to output VCF file.
Performance--num-threads NUM_THREADSNoNumber of threads for worker. (default: 4)
Runtime--verboseNoEnable verbose output.
Runtime--x3NoShow full command line arguments.
Runtime--logfile LOGFILENoPath to the log file. If not specified, messages will only be written to the standard error output.
Runtime--tmp-dir TMP_DIRNoFull path to the directory where temporary files will be stored. (default: .)
Runtime--with-petagene-dir WITH_PETAGENE_DIRNoFull 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. Optionally set the PetaLinkMode environment variable that is used to further configure PetaLink, notably setting it to "+write" to enable outputting compressed BAM and .fastq files.
Runtime--keep-tmpNoDo not delete the directory storing temporary files after completion.
Runtime--no-seccomp-overrideNoDo not override seccomp options for docker.
Runtime--versionNoView compatible software versions.
Runtime--preserve-file-symlinksNoOverride default behavior to keep file symlinks intact and *not* resolve the symlink.