lynnjo
commented
6 months ago Thanks for your feedback. The documentation is incorrect - I will update it. There is no output parameter for this command. The h.vcf files are written to the folder indicated by the gvcf-dir parameter (ie, they are written to the same folder than contains the gvcf files).
Description
Hvcf from PHG created Gvcf
phg gvcf2hvcf \ --db-path /path/to/dbs \ --bed /path/to/bed_file.bed \ --reference-file /my/ref.fasta \ --gvcf-dir /my/gvcf/files \ -o /path/to/hvcf
This is the template command however this command cannot accept a -o option.
Expected behavior
The error messages are going great so far! I'm testing this out without hand holding so hopefully can help with some of the usability.
PHG version
No response