Question: Qustions about Somatic Variant Caller
gravatar for Phoe
14 months ago by
Phoe10 wrote:


I'm new in bioinformatics and I'm curious about something. I've read some papers about somatic variant callers:

(1) Does the somatic variant callers assume that we put the data contained somatic dna sequence (tumor:normal) or they can identify through the allele frequencies no matter what we input?

(2) How many kinds of the algorithm might behind the somatic variant callers? I know VarScan2 relies on heuristic while MuTect or JointSNVMix use Bayesian modeling.

What else could be? Also, what are the pros and cons?

(3) Best Software For Detection Of Somatic Mutations From Matched Tumor:Normal Ngs Data <- This post benefits me a lot, containing the suggestions for "Detection Of Somatic Mutations From Matched Tumor:Normal Ngs Data". But, if there are no tumor and matched normal samples; only the tumor samples. Are there any somatic variant callers recommended?

Thank you.

variant caller snp ngs • 423 views
ADD COMMENTlink written 14 months ago by Phoe10
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