Ryan Layer

I recommend that you use the new lumpy wrapper smoove https://github.com/brentp/smoove > On Jun 7, 2019, at 9:41 AM, nelsonchanhk wrote: > > Hello, > > I've tried lumpy-sv from...

This is tricky. We added those checks b/c people were passing erroneous BAMS. Maybe a better way is to check to see if pe was passed when checking those paramter....

I have no tested this yet, but given the authors match I would expect it work. On Tue, Apr 2, 2019 at 2:06 AM rvaldes wrote: > Have you tested...

Ya, I think that would be a good idea. I don't have much experience with targeted sequencing, but I would suggest you use smoove, our new lumpy wrapper https://github.com/brentp/smoove On...

It’s hard to tell if that is real. The pe depth is very high, but the se depth is not. Try visualizing it in either IGV or our tool called...

I am recommending that people use the new lumpy wrapper smoove https://github.com/brentp/smoove > On Jun 6, 2019, at 2:31 AM, nelsonchanhk wrote: > > Hello, I'm new to lumpy. I've...

I would suggest running lumpy on each sample individually, then merging all of them together with lsort and lmerge from svtools https://github.com/hall-lab/svtools The process is: call and genotype (with svtyper...

Do not bgzip lsort. - lsort all your vcfs, this creates a temp file - lmerge the temp file, this is your full set of SVs - genotype your call...

If you didn't genotype things then you need to use the -r option. On Tue, Jan 8, 2019 at 4:51 AM Jordi Valls Margarit < [email protected]> wrote: > Hi Ryan,...

> On Feb 15, 2019, at 3:37 AM, Jordi Valls Margarit wrote: > > Dear Ryan, > > I have a new question about svtyper... I have 808 samples at...