genotypegvcf
This tool converts variant calls in g.vcf format to VCF format.
$ pbrun genotypegvcf \
--ref Ref.fa \
--in-gvcf input.g.vcf \
--out-vcf output.vcf
$ gatk GenotypeGVCFs -R Ref.fa -V input.g.vcf -O 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 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.
Options specific to this tool
- --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
- --license-file LICENSE_FILE
- --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.
Path to license file license.bin if not in the installation directory.
Do not override seccomp options for docker (default: None).
View compatible software versions.