delly-users

HI I have a Delly output for an INV-withingene event. The gene is on chromosome 5 and it is on the

Thanks for pointing out the location On Thursday, March 7, 2024 at 9:48:24 AM UTC+1 Tobias Rausch

Hello everyone, After getting the output from Delly (and other SV caller), may I know how I get do

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, Can you please be more precise about these parameters: I can't seem to find the information

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-

Hi, Delly has been designed for whole-genome sequencing data. Marked duplicates are excluded from the

Hi Heidi, Depends whether you are interested in somatic or germline SVs. I have put some exemplary

Hi Tobias, Thank you for the response. Regarding 'Not enough windows' error, is this due to

Hi, bcftools merge creates a multi-sample VCF from non-overlapping sample sets. It does not change

Hi Maximus, For human and mouse, these exclude files are available in the delly github repository:

Hi Dell-users Not directly relevant, but was looking to use this thread to request that if anyone is

Ok, thanks. Il giorno mer 29 mar 2023 alle ore 15:49 Tobias Rausch <rausc...@gmail.com> ha

Dear Tobias, Thanks so much for your quick answer. I did indeed find several variant calls in regions

Hi Manuela, The chromosomes in your BAM file (samtools view -H myfileinput.bam) need to match the

Hi Jens, The 2012 paper only covers structural variant detection using short reads. It does not

I am not sure I am doing this right: in the initial `delly call`, I get a few SVs. In one example

Hi everyone, I am looking to discover somatic SV in 50 breast cancer samples (each with a

Dear all, Delly v1.1.3: https://github.com/dellytools/delly/releases Status messages are now on

Dear all, Released Delly v1.0.3: https://github.com/dellytools/delly/releases I've revised

I am not familiar with the Galaxy implementation. To increase sensitivity, you can set the mapping

I call SV as described in "Somatic SV calling", I noticed a reliable DEL (verified in IGV)

Hi Tobias， Thanks for the explanation. I would like to do it with SV calls if this is the better way.