vcfanno
Annotate a VCF file using dbsnp and annotation files (Original VCFANNO Project).
$ pbrun vcfanno \
--in-vcf input.vcf \
--out-vcf output.vcf \
--annotations database.vcf.gz \
--dbsnp dbsnp.vcf.gz
Annotate a VCF using dbsnp and annotation files.
Input/Output file options
- --in-vcf IN_VCF
- --annotations ANNOTATIONS
- --dbsnp DBSNP
- --out-vcf OUT_VCF
Path to the input VCF file to annotate. (default: None)
Option is required.
A prefix and VCF in the format <prefix:/absolute/path/anno.vcf.gz>. INFO fields from <anno.vcf.gz> will be added to the input VCF. This option can be used multiple times and is required if --dbsnp is not used. Annotation VCFs must be bgzipped and tabix indexed. (default: None)
dbSNP file(s) used to annotate the input VCF, passed in the same way as --annotations (A prefix and VCF in the format <prefix:/absolute/path/dbsnp.vcf.gz>). This option can be used multiple times and is required if --annotations is not used. Must be passed separately as special handing is performed to fix errors in the dbSNP VCF. (default: None)
Path to the output annotated VCF file. (default: None)
Option is required.
Tool Options:
- --num-threads NUM_THREADS
Number of parallel threads to pass to vcfanno. (default: 8)
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.