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’s personal 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

Output pretty-print JSON

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