Ryan Layer
Ryan Layer
I am not sure I understand what you are asking. DP is the total depth across a breakpoint. AF is the proportion of chromosomes with the variant in the population...
If you have a large cohort, then you can genotype this SV across those samples with SVTYPER. From those genotypes you can get a AF in that population. On Wed,...
SVTYPER your variant. Then use RO (Reference allele observation count) and AO (Alternate allele observations). On Mon, Aug 13, 2018 at 1:11 AM panzhaodong123 wrote: > Hi,Ryan, > I met...
It's hard to say without seeing an example. > On Aug 19, 2018, at 9:16 PM, ZD Pan wrote: > > Thanks, > And,I want to know why a SV's...
I'm not sure why this is happening. You may want to try the svtool mailing list. > On Aug 19, 2018, at 9:51 PM, ZD Pan wrote: > > chr1...
That is not normal. What is the library? How did you align your reads? > On Dec 16, 2020, at 6:55 PM, yasin-uzun wrote: > > > I first...
Bwa mem? > On Dec 16, 2020, at 8:48 PM, yasin-uzun wrote: > > > Thank you very much for the fast reply. It is Ilumina data. I aligned...
Hm, I’m not sure. It looks like it is not finding split reads, which is surprising. Can you verify they are in there? Check out the Sam spec for more...
Is your split read file empty? > On Dec 16, 2020, at 9:00 PM, yasin-uzun wrote: > > > I tried it both for my own data and NA12878...
You should check out our new wrapper smoove. https://github.com/brentp/smoove On Wed, Dec 16, 2020 at 9:09 PM yasin-uzun wrote: > No actually. Theee split file size is 1.6G. There are...