Import VCF

Import VCF file(s) from Opal file system. Requires that the destination project has a VCF store activated.

opal import-vcf <CREDENTIALS> <OPTIONS> [EXTRAS]

Options

Option Description
--project PROJECT, -pr PROJECT Project name into which genotypes data will be imported
--vcf FILE01 FILE02, -vcf FILE01 FILE02 List of VCF/BCF (optionally compressed) file paths (in Opal file system)

Credentials

Authentication can be done by username/password credentials OR by personal access token OR by certificate/private key pair (two-way SSL authentication).

Option Description
--opal OPAL, -o OPAL Opal server base url
--user USER, -u USER Credentials auth: user name (requires a password)
--password PASSWORD, -p PASSWORD Credentials auth: user password (requires a user name)
--token TOKEN, -tk TOKEN Token auth: User access token
--ssl-cert SSL_CERT, -sc SSL_CERT Two-way SSL auth: certificate/public key file (requires a private key)
--ssl-key SSL_KEY, -sk SSL_KEY Two-way SSL auth: private key file (requires a certificate)

Extras

Option Description
-h, --help Show the command help’s message.
--verbose, -v Verbose output.
--json, -j Pretty JSON formatting of the response.

Example

Import VCF files into the project TEST:

opal import-vcf --opal https://opal-demo.obiba.org --user administrator --password password --project TEST --vcf /path/to/file01.vcf.gz /path/to/file02.vcf.gz