anno export - spiralgenetics/biograph GitHub Wiki

To export an annotation from the vdb, use biograph vdb anno export. This restores the file originally uploaded via vdb anno import.

Use the --aid or -a switch to specify the aid of the annotation you want to export. You can look up the aid for any sample using vdb anno list.

The default output is STDOUT. Use the --output or -o switch to write the VCF to a file.

$ vdb anno export --aid c8d42e04-80ae-415d-a848-2b162dcb7f86 -o ClinVar37.vcf.gz
$ ls -l
-rw-rw-r-- 1 ubuntu ubuntu  33811832 May 27 14:46 ClinVar37.vcf.gz

Getting more help

$ biograph vdb anno export --help
usage: biograph vdb anno export [-h] -a AID [-o OUTPUT]

Export an annotation

optional arguments:
  -h, --help            show this help message and exit
  -a AID, --aid AID     Export the annotation with this AID
  -o OUTPUT, --output OUTPUT
                        Write output to this file (default: STDOUT)