Question: Copy Number Variation Tools
2
gravatar for nayshool
3.2 years ago by
nayshool20
Israel
nayshool20 wrote:

Hi,

We are searching for the best tool for detection of Copy Number Variants and/or Structural Variants from exome seq. We would like to incorporate that tool into out current pipeline. Which are the best tools for exome seq available as for today?

thank you

Omri

ADD COMMENTlink modified 3.2 years ago by Titus910 • written 3.2 years ago by nayshool20
3
gravatar for Eric T.
3.2 years ago by
Eric T.2.6k
San Francisco, CA
Eric T.2.6k wrote:

The bcbio-nextgen documentation describes a pipeline for structural variant calling that is consistent with best practices. Here are the callers that are suitable for exomes:

  • Lumpy, Manta, and DELLY for paired end and split read calling
  • CNVkit for read-depth based CNV calling
  • WHAM for association testing
ADD COMMENTlink modified 3.2 years ago • written 3.2 years ago by Eric T.2.6k
0
gravatar for genebow
3.2 years ago by
genebow160
USA/Chicago
genebow160 wrote:

I have developed an algorithm to compute the copy number of DNA repeats, but not sure if the algorithm can fit your need. You can check the paper and its source code. [Yin, C. (2017). Identification of repeats in DNA sequences using nucleotide distribution uniformity. Journal of Theoretical Biology, 412, 138-145.], Python source code

ADD COMMENTlink written 3.2 years ago by genebow160
0
gravatar for markus.riester
3.2 years ago by
markus.riester490 wrote:

There are a couple of good reviews with links to all important tools, for example a fairly recent one is https://doi.org/10.1093/bib/bbv055.

There is no gold standard and different tools were optimized for very different scenarios. Some tools require matched normals. Some use pool of normals for better coverage normalization. Some support off-targets reads for assays without tiling probes. Some are tumor purity and ploidy aware and provide integer copy numbers. Some tools work better in high-throuput settings than others. Some work better in clinical samples (low purity FFPE samples for example) than others.

A few recent tools not mentioned in the review or in the previous posts: CopywriteR, EXCAVATOR2, GATK4 beta, Sequenza, Facets, PureCN.

ADD COMMENTlink written 3.2 years ago by markus.riester490
0
gravatar for geocarvalho
3.2 years ago by
geocarvalho140
Brazil/Recife
geocarvalho140 wrote:

I'm trying to study Structural Variants in Genome first, but I already noted some softwares for Exome: cnvScan, CoNIFER, exomeCopy, CONTRA, EXCAVATOR2, CODEX, CLAMMS.

ADD COMMENTlink written 3.2 years ago by geocarvalho140
0
gravatar for Titus
3.2 years ago by
Titus910
Titus910 wrote:

I used XHMM which pretty easy to use, looks working well but you need at least around 50 samples to have strong statistics and reduces false positive. As you can see there is a lot of software and no good demonstration (to my knowledge) of the best one. Even this publication https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3484655/ is a bit old i found it a good abstract of the diversity/algorithm.

ADD COMMENTlink written 3.2 years ago by Titus910
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