Dave Larson

For context, I'm seeing this error when running Smoove.

Yeah, that's what I'd expect. They're not actually multiple samples though...just mislabeled single samples. If by happy circumstance it was all erroneously analyzed as a single sample, then that may...

I'm afraid I don't understand the question. I believe DP is reported for your sample in the FORMAT field. Could you clarify what you're looking for?

You are correct in your assumptions, but there isn't a documented list. Looking quickly through the code, it would appear that MATEID, END, CIPOS, CIEND and SVTYPE are all required....

I think there is likely to be a version of svtyper that does this at some point, but I'm not sure when that may happen. I've run into the same...

@dr-ashu-geno - It's been too long for me to recall for certain, but I'm fairly sure I calculated outside of svtools and then simply added the new tags to the...

svtyper doesn't do this and isn't likely to in the near future. We've put together another package, svtools, that supports this type of functionality through the merging of lumpy calls....

Hi @thomasfaraut - we're aware of the upcoming deprecation of python2 and plan to provide a python3 version before then, but have no immediate plans to do so. At this...

Yes, we've done something similar in svtools. See https://github.com/hall-lab/svtools/blob/master/svtools/utils.py for the class we put together to handle this. We could apply the same strategy here with a bit of refactoring.

I'll leave this open until the feature is added.