Open rickymagner opened 6 months ago
Most short-read SV callers do not attempt SV breakpoint assembly and that is, what delly stores in INFO/CONSENSUS. INFO/CONSBP indicates the SV breakpoint position on that consensus sequence.
For long-reads, you may have SV breakpoint assemblies and these you can map using minimap2 to your reference genome. From these assembly mappings you can create a delly VCF using ...
delly asm ...
...which you can then genotype. The asm subcommand is indeed not document yet because it's under development.
Hi, I'm trying to genotype an SV VCF with Delly and getting this error:
How can I add these fields to my VCF? I don't mind writing a script to do it, but just wanted to check what they're supposed to be. I'm trying to run:
The SV VCF I'm using wasn't produced by Delly, but I wanted to try genotyping it using Delly and my reads for testing. It doesn't seem like the README covers this case unless I missed something. Thanks!