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.