Fritz Sedlazeck

Wait you just want to know if the SV exist in half of the reads ? Take samplot or IGV directly .. without phasing. Whatshap is needed to tag the...

Thanks we can reproduce this now also here.. @lfpaulin is working on that. Hope we have a fix on the next verison. We found the issue , which is basically...

We have a working prototype that goes through testing right now. It looks like we resolved it. We hope that we can roll out that new version next week. Thanks...

So this is still something we are investigating. @lfpaulin can maybe expand a bit more... the SNF file holds all variants but they have set filters.. These filters can be...

Sorry for that. I can cross check with the team if there is a mode to rescue form the SNF file.. the SV should be in there but has already...

Yeah... I also have a similar situation. Meeting with @hermannromanek next monday and will discuss. Stay tune pls. Fritz

@hermannromanek can we close this or is there still something we need to change ? Thanks Fritz

I think @hermannromanek you take care of this and its released already right ? Thanks Frit z

Yeah Sniffles right now filters for 20 or higher MQ... thats a parameter that you could change. We are not maintaining NGMLR anymore... sorry Fritz

Thanks @kaltinel this is indeed very interesting for us too but we have not tested this. In theory it should work,but I would set the min SV size to 1000bp...