Genotyping a given SV VCF with Delly

[rickymagner]

Hi, I'm trying to genotype an SV VCF with Delly and getting this error:

Error: Delly genotyping requires local SV assembly (INFO/CONSENSUS) and breakpoint (INFO/CONSBP) introduced in delly v1.1.7!

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:

delly call \
    -g ref.fasta \
    -v input.vcf.gz \
    -o delly.bcf \
    input.bam

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!

[tobiasrausch]

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.