Export VCF

Export VCF files in Opal file system.

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

Options

Option Description
--project PROJECT, -pr PROJECT Project name from which genotypes data will be exported
--vcf FILE01 FILE02, -vcf FILE01 FILE02 List of VCF/BCF file names
--destination DESTINATION, -d DESTINATION Destination folder (in Opal file system)
--filter-table FILTER -f FILTER Participant table name to be used to filter the samples by participant ID (only relevant if there is a sample-participant mapping defined)
--no-case-controls, -nocc Do not include case control samples (only relevant if there is a sample-participant mapping defined)

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

Export VCF files into the user’s export directory, omitting control samples:

opal export-vcf --opal https://opal-demo.obiba.org --user administrator --password password --project TEST --vcf FILE01 FILE02 --destination /home/administrator/export --filter-table TEST.mapping --no-case-controls