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.
# This command assumes all the inputs are in
and all the outputs go to
.
$ 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}
$ 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
- --in-gvcf IN_GVCF
- --in-selectvariants-dir IN_SELECTVARIANTS_DIR
- --out-vcf OUT_VCF
Path to the reference file. (default: None)
Option is required.
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)
Path to output directory of selectvariants. (default: None)
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
- --tmp-dir TMP_DIR
- --with-petagene-dir WITH_PETAGENE_DIR
- --keep-tmp
- --no-seccomp-override
- --version
Path to the log file. If not specified, messages will only be written to the standard error output. (default: None)
Full path to the directory where temporary files will be stored.
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)
Do not delete the directory storing temporary files after completion.
Do not override seccomp options for docker (default: None).
View compatible software versions.