Ryan Layer

Is this because the genome is circular? On Thu, Nov 30, 2017 at 1:26 AM, Zhongliang wrote: > OK, thanks. > But speedsed for bacteria make me confused on the...

What is the coverage? On Tue, Oct 19, 2021 at 11:02 AM pabloangulo7 ***@***.***> wrote: > Hello, > > I would like to use this tool in an haploid organism....

Oh that more than I expected. What species? There should be no issue given those coverages. Try using smoove. It makes the whole process much easier. https://github.com/brentp/smoove > On Oct...

That would be useful, but I think the best place fo etc this output would be in SVTyper. We are better able to determine which reads support the SV in...

You seem to be missing some of the tools needed to compile. Try installing autoheader and autoconf. On Tue, Dec 26, 2017 at 10:57 PM, LikithReddy wrote: > Hi, I"m...

Looks like an issues with your samtools. See https://github.com/merenlab/anvio/issues/1479 On Fri, Apr 23, 2021 at 4:42 AM assane-mbodj ***@***.***> wrote: > Hello I am new in programming and I wanted...

If you are referring to the N in the ALT field, we do that instead of putting the sequence. If you are referring to the fact that all of your...

It was a false positive that was corrected by svtyper and yes, filter by allele count. > On Apr 24, 2021, at 9:11 PM, shuiyanwu778 ***@***.***> wrote: > > ...

That is strange. It is as if it did not grab the command line argument correctly. I suggest you use smooch. https://github.com/brentp/smoove It is a much better wrapper than lumpyexpress...

Many of the SVs are very large. Including the deleted sequences in the ALT field would make manual inspecting the VCF very difficult. On Mon, Aug 28, 2023 at 11:37 ...