delly-users

Hi Quan Cheng, Delly is not a general purpose genotyper because the genotyping function in delly

Hi Andrea, Sounds like the translocation is flanked by repeats or a segdup or I may misunderstand

Thank you for your kind answer and for clarifying the meaning of the field, I appreciate it. Best,

Great, thanks for the hint!!! wtorek, 11 lutego 2025 o 10:38:04 UTC+1 Tobias Rausch napisał(a): I

Hi all! I am very interested in the following question! I can only contribute telling you that I find

Dear Patricie, So far I am using the *.r101.s501.* maps by default. I am indeed experimenting with

On Sunday, November 24, 2024 at 8:07:41 PM UTC+1 Tobias Rausch wrote: Hi Pierre, For the delly call

Hi, I have a question related to this. Given that XY samples have expected copies of 1 on X,Y

Hi, I can confirm that for CNV calling delly only uses the FORMAT:CN field at the moment. That's

Hi Tobias Rausch, I am running the germline CNV calling command from the GitHub tutorial. I have all

Dear Tobias Rausch, I am running the germline CNV calling command from the GitHub tutorial. I have

Hmm, that's puzzling. In general, I would recommend to only mark duplicates and not to remove

Hi Tobias, Thanks for your reply. For short reads NGS, may I know what the formal procedures using

Right, my bad, I took the header from a file before środa, 28 sierpnia 2024 o 13:58:01 UTC+2 Tobias

Hi Tobias, thank you for your answer. I already understand. I thought that the mappability maps must

I use Ensembl's VEP. It works nice directly with the vcf generated by delly. I didn't try

Hi, To filter delly's output we should do: Apply the germline SV filter which requires at least

Hi group, I am trying to run delly cnv on my short-read data, but it fails right at the beginning

In general, it's better to run multiple patients in parallel instead of trying to run delly with

The functional effects of inversions are difficult to predict. In general, whole-gene inversions are

Hi there, How should I interpret confidence intervals for delly variants? What distribution is used

FORMAT/CN is the read-depth based estimated copy-number (FORMAT/RDCN as a float). On Mon, Jan 29,

As written in the README, you should use a recursive clone: git clone --recursive https://github.com/

The -t command-line parameter is indeed somewhat related to tumor purity, ploidy and subclonality. To

Hi Mattias, Delly has 2 phases, (i) SV site discovery and (ii) SV genotyping. For the SV site

Hi Tobias Thank you for delly2, it is very polished and it is great you maintain this forum. I have

You need to install the Boost libraries to compile from source. On Wed, Nov 1, 2023 at 7:30 PM Cactus

Hi group, I am using delly/1.1.6 to call somatic CNV. I am a bit confused with the output as you can

Thanks, it worked. Sorry for my late reply! On Mon, Sep 25, 2023 at 2:14 AM Tobias Rausch <

Hi, RC is the coverage inside the SV and RCL and RCR the values to the Left and Right. The copy-