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.

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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}

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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. (default: None)

Option is required.

--out-vcf OUT_VCF

Path to output VCF file. (default: None)

Option is required.

Options specific to this tool

(none)

Performance 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 2024, Nvidia. Last updated on Jan 9, 2024.