genotypegvcf

This tool converts variant calls in g.vcf format to VCF format.

Quick Start

$ pbrun genotypegvcf \
    --ref Ref.fa \
    --in-gvcf input.g.vcf \
    --out-vcf output.vcf

Compatible CPU GATK4 Command

$ gatk GenotypeGVCFs -R Ref.fa -V input.g.vcf -O 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 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.

Options specific to this tool

--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.

--license-file LICENSE_FILE

Path to license file license.bin if not in the installation directory.

--no-seccomp-override

Do not override seccomp options for docker (default: None).

--version

View compatible software versions.