vcf export - spiralgenetics/biograph GitHub Wiki

To export a VCF file from the vdb, use biograph vdb vcf export. This restores the file originally uploaded via vdb vcf import.

Use the --aid or -a switch to specify the aid of the VCF you want to export. The aid is required since there may be multiple VCFs present for a given sample name. You can look up the aid for any sample using vdb vcf list.

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

$ biograph vdb vcf export -a 2e7a0129-13a5-44b6-8594-2fc2e6c80e6c -o HG002.vcf.gz
$ ls -l
-rw-rw-r-- 1 ubuntu ubuntu  364675394 May 14 15:32 HG002.vcf.gz

Getting more help

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

Export a VCF

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