vcf list - spiralgenetics/biograph GitHub Wiki

To see a list of all available VCFs, use biograph vdb vcf list. This displays the sample name, import date, reference, variant count, and aid for every available VCF.

$ biograph vdb vcf list
sample_name  imported_on          refname  variant_count aid                                  description
HG002        2021-05-14 15:54:31  hs37d5   4578933       7df5a719-47ed-4cb8-be1b-b4c09864fc6f HG002 on hs37d5
HG002        2021-05-13 14:31:21  grch38   4556521       2e7a0129-13a5-44b6-8594-2fc2e6c80e6c
HG003        2021-05-13 14:32:34  grch38   4350342       a98626d6-758b-468d-add9-fbfbac47d207
HG004        2021-05-13 14:33:43  grch38   4632093       9a174215-8fc5-4c6f-bc4b-134654f65b99

Note that any number of VCFs may be uploaded per sample, so there may be multiple VCFs present for a given sample name.

As the list of VCFs grows, it can be useful to filter the list to only match samples with a given prefix using the --sample or -s option.

$ biograph vdb vcf list --sample HG002
sample_name  imported_on          refname  variant_count aid                                  description
HG002        2021-05-14 15:54:31  hs37d5   4578933       7df5a719-47ed-4cb8-be1b-b4c09864fc6f HG002 on hs37d5
HG002        2021-05-13 14:31:21  grch38   4556521       2e7a0129-13a5-44b6-8594-2fc2e6c80e6c

Getting more help

$ biograph vdb vcf list --help
usage: biograph vdb vcf list [-h] [-s SAMPLE]

List all available VCFs

optional arguments:
  -h, --help            show this help message and exit
  -s SAMPLE, --sample SAMPLE
                        Only list VCFs with this sample name prefix