vcfanno

Annotate a VCF file using dbsnp and annotation files (Original VCFANNO Project).

Quick Start

$ pbrun vcfanno \
    --in-vcf input.vcf \
    --out-vcf output.vcf \
    --annotations  database.vcf.gz \
    --dbsnp dbsnp.vcf.gz

vcfanno Reference

Annotate a VCF using dbsnp and annotation files.

Input/Output file options

--in-vcf IN_VCF

Path to the input VCF file to annotate. (default: None)

Option is required.

--annotations ANNOTATIONS

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 DBSNP

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)

--out-vcf OUT_VCF

Path to the output annotated VCF file. (default: None)

Option is required.

Options specific to this tool

--num-threads NUM_THREADS

Number of parallel threads to pass to vcfanno. (default: 8)

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.