Clara Parabricks v4.0.1
v4.0.1

genotypegvcf

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.

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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}

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

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.

© Copyright 2022, Nvidia. Last updated on Feb 22, 2023.