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 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:4.3.2-1 (OR nvcr.io/nvidia/clara/clara-parabricks:4.3.2-1.grace) \
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
-
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.