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