Daniel Cameron

Shouldn't the downstream impacts be within the scope of Variant Annotation and not Variant Representation?

While the possible symbolic alternative alleles header definitions are defined in the section 1.4.5, the actual use of these ID strings (and the requirement for angle bracketing ) is defined...

>Hence here setting ID vs using ID are different. Correct. A VCF record is still valid even if it's missing the corresponding DEL header (but this is not recommended as...

How does this proposal handle scatter-gather/map-reduce pipelines? You end up with different reads from the same `@PG` being processed by different parts of a pipeline. Currently implementation will usually just...

No I didn't get around to doing this. I did a lot of benchmarking (PMID: 31324872) and came to the conclusion that a) GRIDSS and manta (the ones that incorporate...

If it's just GRIDSS calls from multiple samples, merging should be relatively straight-forward since you don't have to deal with the mess of merging from multiple callers each of which...

> but the other SV caller also improves above that for certain SV that are missed initially. We also found you could improve performance with a simple X of Y...

I get the distinct feeling that ensemble calling is popular amougst the large consortia for political reasons. The last time I attempting to convince a consortium I was involved in...

@d-cameron I know a population can be merged using structural variant annotation R, but it would be nice to have them as a VCF for a few reasons - to...

> If two caller agree on the same SV its more likely to be correct. This issue with this approach is that similar callers make the same FP calls (https://www.nature.com/articles/s41467-019-11146-4/figures/3)....