genotypegvcf
This tool converts variant calls in g.vcf format to VCF format.
<br>
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 <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:v4.0.1-1 \
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.
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.