Open torchij opened 4 years ago
@torchij this is definitely something I can look into adding. @calchoo already has investigated this some for our use cases.
The reason we didn't default to this initially is that VCF is pretty limited when it comes to supporting SVs. It also isn't very readable straight out of the box.
However it would likely be possible to have and an additional or alternative output format.
Hi @creisle, thanks for the response, I greatly look forward to this option. Agreed, the VCF format for structural variants and CNV is restrictive, but it seems to be picking up steam... Thanks again
Modern SV callers are increasingly adapting the VCF specification (https://samtools.github.io/hts-specs/VCFv4.2.pdf) as an output format for SVs. I think this would be a highly valuable option to add to MAVIS. This would allow for a more seamless transition between MAVIS results and downstream analysis.