Body: <p>I am a beginner in this field. I would like to know which is the best way to get all the mutations from a certain sample. At this point, I am considering using GATK (<a href="https://gatk.broadinstitute.org/hc/en-us" rel="nofollow noreferrer">here</a>) and Maftools (<a href="https://bioconductor.org/packages/release/bioc/vignettes/maftools/inst/doc/maftools.html#1_Introduction" rel="nofollow noreferrer">here</a>). I don't know which method is better, or are there any other better tools you would recommend?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-03-28T18:36:55.490Z
Comments.Text: MAFtools is not a variant calling tool. Google "benchmark somatic variant callers" and read some papers - MuTect2, SomaticSniper, VarScan2, Strelka etc are some relevant tools.
Comments.UserDisplayName: Ram RS
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-03-29T03:10:08.090Z
Comments.Text: What organism are you working on, i.e. your sample? This has an enormous impact on the approach and the tools.
Comments.UserDisplayName: M__
Tags: <phylogenetics><variant-calling><gatk><maftools>
Title: What is the best tools to find all the somatic mutations?
ThreadText: # What is the best tools to find all the somatic mutations?
  
  (Asked by: username_0 on 2022-03-28)
  
  I am a beginner in this field. I would like to know which is the best way to get all the mutations from a certain sample. At this point, I am considering using GATK ([here](https://gatk.broadinstitute.org/hc/en-us)) and Maftools ([here](https://bioconductor.org/packages/release/bioc/vignettes/maftools/inst/doc/maftools.html#1_Introduction)). I don't know which method is better, or are there any other better tools you would recommend?
  
  **Tags:** phylogenetics, variant-calling, gatk, maftools
  
  > **Comments:**
  > **username_1**: MAFtools is not a variant calling tool. Google "benchmark somatic variant callers" and read some papers - MuTect2, SomaticSniper, VarScan2, Strelka etc are some relevant tools.  
  > **username_2**: What organism are you working on, i.e. your sample? This has an enormous impact on the approach and the tools.  
  
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  ## 0 answers
  
  