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.
See the genotypegvcf Reference section for a detailed listing of all available options.
# This command assumes all the inputs are in the current working directory and all the outputs go to the same place.
docker run --rm --gpus all --volume $(pwd):/workdir --volume $(pwd):/outputdir \
--workdir /workdir \
nvcr.io/nvidia/clara/clara-parabricks:4.5.1-1 \
pbrun genotypegvcf \
--ref /workdir/${REFERENCE_FILE} \
--in-gvcf /workdir/${INPUT_GVCF_FILE} \
--out-vcf /outputdir/${OUTPUT_VCF}
$ gatk GenotypeGVCFs \
-R <INPUT_DIR>/${REFERENCE_FILE} \
-V <INPUT_DIR>/${INPUT_GVCF_FILE} \
-O <OUTPUT_DIR>/${OUTPUT_VCF}
Convert GVCF to VCF.
Type | Name | Required? | Description |
|---|---|---|---|
| I/O | ‑‑ref REF | Yes | Path to the reference file. |
| I/O | ‑‑in‑gvcf IN_GVCF | Yes | Input a g.vcf or g.vcf.gz file that will be converted to VCF. Required. |
| I/O | ‑‑out‑vcf OUT_VCF | Yes | Path to output VCF file. |
| Performance | ‑‑num‑threads NUM_THREADS | No | Number of threads for worker. (default: 4) |
| Runtime | ‑‑verbose | No | Enable verbose output. |
| Runtime | ‑‑x3 | No | Show full command line arguments. |
| Runtime | ‑‑logfile LOGFILE | No | Path to the log file. If not specified, messages will only be written to the standard error output. |
| Runtime | ‑‑tmp‑dir TMP_DIR | No | Full path to the directory where temporary files will be stored. (default: .) |
| Runtime | ‑‑with‑petagene‑dir WITH_PETAGENE_DIR | No | 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. 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‑tmp | No | Do not delete the directory storing temporary files after completion. |
| Runtime | ‑‑no‑seccomp‑override | No | Do not override seccomp options for docker. |
| Runtime | ‑‑version | No | View compatible software versions. |