Ryan Layer

All of those alignments have MAPQ=0, which lumpy ignores. There is a cmd line setting for mapq, but zero will give you a ton of false positives. > On Dec...

Can you plot a few of your SVs to see if there should be SR support? IGV or samplot (shameless self promotion, https://github.com/ryanlayer/samplot) are good options. On Fri, Dec 18,...

It looks like like your images didn’t make it > On Dec 18, 2020, at 1:31 PM, yasin-uzun wrote: > >  > Thank you. Samplot seems like a great...

Seems so. Check the strands on these calls, you should have a mix of -- and ++ paired-end reads. On Wed, Sep 4, 2019 at 11:11 PM Yiguan wrote: >...

I would be a bit suspect if there is no drop in coverage. Does it overlap a repetitive region? > On Jul 2, 2019, at 11:53 AM, shannjiang wrote: >...

Each “-pe” will get its own histogram, so separating out the different libraries with different properties is a good move. Do not merge thing back together. Each sample should have...

I think that you are getting bogged down in low complexity regions. Do you have these annotated for your genomes? On Sun, Feb 3, 2019 at 12:23 PM Gregg WC...

I am not really sure what I expect here, but it is good news that excluding noisy regions reduces the number of calls. What % of your calls are BNDs...

Yes, but you need to go search for B. On Tue, Mar 5, 2019 at 11:35 AM Mark Dunne wrote: > Hi, > > Suppose I have a translocation from...

I recommend that you use the new lumpy wrapper smoove https://github.com/brentp/smoove > On Jun 22, 2019, at 9:08 AM, tyyiyi wrote: > > I also have the same problem, have...