<p>What is the state-of-the-art to obtain SNVs from circulating tumor DNA after Illumina sequencing? This is, finding a list of nucleotide locations that show tumour SNVs filtered out of any germline polymorphisms.</p>

<p>Found so far:</p>

<ul>
<li><p><a href="https://www.ncbi.nlm.nih.gov/pubmed/27531099" rel="nofollow noreferrer" title="article">SiNVICT: ultra-sensitive detection of single nucleotide variants and
indels in circulating tumour DNA.</a></p></li>
<li><p><a href="https://github.com/OpenGene/ctdna-pipeline" rel="nofollow noreferrer" title="code">OpenGene/ctdna-pipeline</a></p></li>
<li><p><a href="https://github.com/mikessh/mageri" rel="nofollow noreferrer" title="code">MAGERI</a>: <a href="http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005480" rel="nofollow noreferrer" title="article">article</a></p></li>
<li><p><a href="https://github.com/broadinstitute/mutect" rel="nofollow noreferrer" title="code">MuTect</a>: running it against a synthetic normal for unmatched cfDNA samples that don't have normal, then filtering for 1000G germline mutations.</p></li>
<li><p><a href="https://github.com/cancerit/CaVEMan" rel="nofollow noreferrer" title="code">CaVEMan</a>: running it against a reference normal for unmatched cfDNA samples that don't have equivalent normal, then filtering for 1000G germline mutations.</p></li>
<li><p><a href="http://bioconductor.org/packages/ShearWater" rel="nofollow noreferrer" title="Bioconductor">ShearWater</a>: <a href="https://bioconductor.org/packages/3.7/bioc/vignettes/deepSNV/inst/doc/shearwaterML.html" rel="nofollow noreferrer" title="vignette">corrects against germline mutations by training against a set of healthy normal samples.</a></p></li>
</ul>

CC BY-SA 3.0
2018-03-28T07:30:08.163Z
Do you think you can narrow a bit more? In what aspects are you interested? What tool(s) have you tried?
llrs
CC BY-SA 3.0
2018-03-28T08:13:43.410Z
@Llopis I have now extended the question and added 3 more pieces of software that I found relevant.
719016
CC BY-SA 3.0
2018-03-28T08:26:40.220Z
Yes, precisely because you can grow the list *ad infinitum* I wanted you to narrow the question. In general those open ended questions don't work well in the StackExchange format because they don't have an answerable with a correct answer. And tend to results in a list of software, that although interesting and useful it might fit better for a blog or other type of resources. That's why I asked if you have some problem with any of these tools.
llrs
CC BY-SA 3.0
2018-03-28T08:34:40.263Z
The problem is that, presumably, all of these are "state of the art", so choosing one will be largely a question of opinion. Therefore, this is a very interesting discussion, but not really something that can be given a definitive answer of the sort that the Stack Exchange model requires.
terdon
<snv>
state-of-the-art methods to obtain SNVs from circulating tumor DNA?
# state-of-the-art methods to obtain SNVs from circulating tumor DNA?

(Asked by: username_0 on 2018-03-28)

What is the state-of-the-art to obtain SNVs from circulating tumor DNA after Illumina sequencing? This is, finding a list of nucleotide locations that show tumour SNVs filtered out of any germline polymorphisms.

Found so far:

* [SiNVICT: ultra-sensitive detection of single nucleotide variants and
  indels in circulating tumour DNA.](https://www.ncbi.nlm.nih.gov/pubmed/27531099 "article")
* [OpenGene/ctdna-pipeline](https://github.com/OpenGene/ctdna-pipeline "code")
* [MAGERI](https://github.com/mikessh/mageri "code"): [article](http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005480 "article")
* [MuTect](https://github.com/broadinstitute/mutect "code"): running it against a synthetic normal for unmatched cfDNA samples that don't have normal, then filtering for 1000G germline mutations.
* [CaVEMan](https://github.com/cancerit/CaVEMan "code"): running it against a reference normal for unmatched cfDNA samples that don't have equivalent normal, then filtering for 1000G germline mutations.
* [ShearWater](http://bioconductor.org/packages/ShearWater "Bioconductor"): [corrects against germline mutations by training against a set of healthy normal samples.](https://bioconductor.org/packages/3.7/bioc/vignettes/deepSNV/inst/doc/shearwaterML.html "vignette")

**Tags:** snv
> **Comments:**
> **username_1**: Do you think you can narrow a bit more? In what aspects are you interested? What tool(s) have you tried?  
> **username_0**: @Llopis I have now extended the question and added 3 more pieces of software that I found relevant.  
> **username_1**: Yes, precisely because you can grow the list *ad infinitum* I wanted you to narrow the question. In general those open ended questions don't work well in the StackExchange format because they don't have an answerable with a correct answer. And tend to results in a list of software, that although interesting and useful it might fit better for a blog or other type of resources. That's why I asked if you have some problem with any of these tools.  
> **username_2**: The problem is that, presumably, all of these are "state of the art", so choosing one will be largely a question of opinion. Therefore, this is a very interesting discussion, but not really something that can be given a definitive answer of the sort that the Stack Exchange model requires.  

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## 0 answers

