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

 # 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:4.0.0-1 \
    pbrun genotypegvcf \
    --ref /workdir/${REFERENCE_FILE} \
    --in-gvcf /workdir/${INPUT_GVCF_FILE} \
    --out-vcf /outputdir/${OUTPUT_VCF}

Compatible CPU GATK4 Command

$ 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.