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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:

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  • $\begingroup$ Do you think you can narrow a bit more? In what aspects are you interested? What tool(s) have you tried? $\endgroup$
    – llrs
    Mar 28, 2018 at 7:30
  • $\begingroup$ @Llopis I have now extended the question and added 3 more pieces of software that I found relevant. $\endgroup$
    – 719016
    Mar 28, 2018 at 8:13
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    $\begingroup$ 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. $\endgroup$
    – llrs
    Mar 28, 2018 at 8:26
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    $\begingroup$ 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. $\endgroup$
    – terdon
    Mar 28, 2018 at 8:34

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