Question: Tools for SV & CNV detection
1
gravatar for alons
3.2 years ago by
alons270
Rehovot
alons270 wrote:

Hi all,

We're performing NGS on cancer DNA samples with a custom panel of target regions in different genes. 

From your experience & knowledge, which tools do you recommend using for our purpose:

1. Finding structural variants (SVs) such as inversions, large indels, translocations, tandem duplications, etc. 

2. CNV (copy number variantion) discovery for only a single sample (many tools I've found were for multiple samples).

If i'm not mistaken I should look for tools that are suitable for exome data rather than whole genome because of our sequencing methods and custom panel.

Thank you very much in advance!



I realize this has been somewhat asked before but the posts I've found were at least 2-3 years old and didn't elaborate on cancer genomics or exome sequencing. It was also unclear to me which CNV discovery tools are suitable for single samples. I hope this isn't out of line.

 

 

 

ADD COMMENTlink modified 3.2 years ago by Leandro Lima920 • written 3.2 years ago by alons270
1

For CNV, you can try "conumee" package. 

ADD REPLYlink modified 3.2 years ago • written 3.2 years ago by Tanvir Ahamed 270

Googled it, will check it out.

ADD REPLYlink modified 3.2 years ago • written 3.2 years ago by alons270

Checked it. Seems like it's not suitable for NGS data.

ADD REPLYlink written 3.2 years ago by alons270
3
gravatar for Eric T.
3.2 years ago by
Eric T.2.4k
San Francisco, CA
Eric T.2.4k wrote:

Lumpy, Delly, Manta, and Pindel are good for detecting structural variation and will work on exome/targeted samples. For CNV detection, some recent review articles give an overview of what's available for your application:

These articles are not comprehensive. A couple of tools not mentioned there but worth checking out are CopywriteR (Bioconductor) and CNVkit (mine; Unix command line) -- these are relevant if you're using hybrid capture, but less so for targeted amplicon capture. In the latter case, try OncoCNV.

In general you can get a good list of tools that are worth using by looking at existing validated pipelines like bcbio-nextgen and speedseq. Even if you don't use these pipelines directly, you can learn from others' experience by reading the documentation they provide.

ADD COMMENTlink modified 3.2 years ago • written 3.2 years ago by Eric T.2.4k

Thank you very much for the detailed answer!
We're already looking to use Pindel & Delly, will definitely check out Lumpy, Manta and the others.
Your program, CNVkit, seems to be relevant actually because we're using hybrid capture.

ADD REPLYlink modified 3.1 years ago • written 3.2 years ago by alons270
1

Re: Manta, note default configuration is WGS -- enrichment/panel analysis requires `--exome` config option:

https://github.com/Illumina/manta/blob/v0.29.3/src/markdown/mantaUserGuide.md#exometargeted

ADD REPLYlink written 3.2 years ago by Chris Saunders170

Thanks, we might try Manta next. Will keep that in mind!

ADD REPLYlink written 3.2 years ago by alons270
2
gravatar for Chris Miller
3.2 years ago by
Chris Miller20k
Washington University in St. Louis, MO
Chris Miller20k wrote:

A collaborator made cc2 (https://github.com/abelhj/cc2) for copy number calling from panel sequencing (using a panel of normals run on the same panel). I can't offer specific advice on using it, but their results have always been really nice.

 

ADD COMMENTlink modified 3.2 years ago • written 3.2 years ago by Chris Miller20k

Thanks! I will check it out.

ADD REPLYlink written 3.2 years ago by alons270
1
gravatar for Leandro Lima
3.2 years ago by
Leandro Lima920
San Francisco, CA
Leandro Lima920 wrote:

I also recommend SVDetect.

ADD COMMENTlink written 3.2 years ago by Leandro Lima920

Thanks. I'm reading about it now. From your experience, in terms of speed, how does it compare to the other SV detection programs?

ADD REPLYlink modified 3.2 years ago • written 3.2 years ago by alons270
1

Alons, I haven't compared speed, but for me it works very well.

Maybe it would be good for you to take a look at this paper:

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0059128

Regards,

Leandro

ADD REPLYlink written 3.2 years ago by Leandro Lima920

@Leandro Lima: I would like to discuss a problem i am facing during my analysis. I have BAM files (Mate-pair, ~3GB, after pre-processing step). I tried to run SVDetect on 64GB and 128GB machine but every time program crashes during "links2compare" process due to high memory usage.

Have you faced this memory related issue ever ? Any recommendation will be helpful to carry my work to next level.

P.S. I am using SVDetect_r0.8b with multiple threads.

Thanks Samarth

ADD REPLYlink modified 2.8 years ago • written 2.8 years ago by Samarth Kulshrestha170

Hi Samarth.

How much memory are you allocating for each thread?

BTW, did you also try Lumpy and CNVnator?

Leandro

ADD REPLYlink modified 2.8 years ago • written 2.8 years ago by Leandro Lima920
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