Biostar Beta. Not for public use.
Tools for SV & CNV detection
1
Entering edit mode
14 months ago
alons • 270
Rehovot

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
1
Entering edit mode

For CNV, you can try "conumee" package.

ADD REPLYlink
0
Entering edit mode

Googled it, will check it out.

ADD REPLYlink
0
Entering edit mode

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

ADD REPLYlink
3
Entering edit mode
13 months ago
Eric T. ♦ 2.4k
San Francisco, CA

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
0
Entering edit mode

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
1
Entering edit mode

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
0
Entering edit mode

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

ADD REPLYlink
2
Entering edit mode
13 months ago
Washington University in St. Louis, MO

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
0
Entering edit mode

Thanks! I will check it out.

ADD REPLYlink
1
Entering edit mode
12 months ago
Leandro Lima • 920
San Francisco, CA

I also recommend SVDetect.

ADD COMMENTlink
0
Entering edit mode

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
1
Entering edit mode

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
0
Entering edit mode

@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
0
Entering edit mode

Hi Samarth.

How much memory are you allocating for each thread?

BTW, did you also try Lumpy and CNVnator?

Leandro

ADD REPLYlink

Login before adding your answer.

Similar Posts
Loading Similar Posts
Powered by the version 2.1