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 name into which genotypes data will be imported |
|
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 server base url |
|
Credentials auth: user name (requires a password) |
|
Credentials auth: user password (requires a user name) |
|
Token auth: user’s personal access token |
|
Two-way SSL auth: certificate/public key file (requires a private key) |
|
Two-way SSL auth: private key file (requires a certificate) |
Extras
Option |
Description |
---|---|
|
Show the command help’s message. |
|
Verbose output. |
|
Output pretty-print JSON |
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