Nancy F. Hansen

It's true there is redundancy in the unfiltered example, but the het variant marked as phased is essentially contained in the second (also het) unphased one, so why would hap.py...

Hi George. Thanks for reporting this. Why is "999" in your ALT field for the second file? I need to look at the code, but I think any line with...

As another note, SVmerge will in general consider deletions without the sequence only when you have an "END" tag in the INFO field (which I see you do for both...

Hi @yueyaog. That's clearly a bug--can you provide me the initial VCF entry and the reference it's aligned to?

Thanks for reporting this error. It looks like the program is dying on a problematic SV, so the ~1000 SVs you got were most likely the first ones in your...

Thanks so much! I knew there had to be a way, but couldn't guess it. --Nancy

I actually spent quite a bit of time reading the manual, but I didn't catch the one place that you use the Gfa segment method, in a section titled "Renaming...

Thanks Giorgio. We'll have to agree to disagree then, because all I see in section 3.2 is methods that return strings, when I wanted a method to return the Segment...

Hi Joe--thanks for the question. The svmerge command only compares neighboring structural variants in pairs, constructing the inferred alternate haplotypes by applying the SV to the reference for each and...