triocombinegvcf
Combines two or three GVCF samples in a fast way.
$ pbrun triocombinegvcf \
--ref Ref.fa \
--in-gvcf father.g.vcf \
--in-gvcf mother.g.vcf \
--in-gvcf child.g.vcf \
--out-variants combined.g.vcf
$ gatk CombineGVCFs -R Ref.fa -V father.g.vcf -V mother.g.vcf \
-V child.g.vcf -O combined.g.vcf
Run trioCombineGVCF on 2 or 3 GVCF files.
Input/Output file options
- --ref REF
- --in-gvcf IN_GVCF
- --out-variants OUT_VARIANTS
Path to the reference file. (default: None)
Option is required.
Path to g.vcf or g.vcf.gz file. Option can be used 2 or 3 times. (default: None)
Option is required.
Path to the output GVCF. (default: None)
Option is required.
Options specific to this tool
(none)
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.