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bcgsc / mavis

Merging, Annotation, Validation, and Illustration of Structural variants
http://mavis.bcgsc.ca
GNU General Public License v3.0
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Add option for standardized VCF output #201

Open torchij opened 4 years ago

torchij commented 4 years ago

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.

creisle commented 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.

torchij commented 4 years ago

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