Answers.Body: <p>Those will have to be treated as separate analysis.  You can use Mutect or VarScan for the matched samples and the tools listed in the <a href="https://bioinformatics.stackexchange.com/questions/2744/somatic-tumor-only-variant-calling">other question</a> for the unmatched samples however that means that you won't be able to compare the results easily.  If the inter-sample comparison is important you will have to run all samples as unmatched.  Personally I have used LoFreq for somatic variant detection with some success.  It is very sensitive so the false positive rate can be high depending on how noisy your data is.</p>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-12-13T18:49:27.003Z
Answers.LastActivityDate: 2017-12-13T18:49:27.003Z
Answers.UserDisplayName: Bioathlete
Body: <p>I have a set of whole genome sequencing samples, some of which have matched normal while some not. I want to call somatic mutations on non-coding regions.</p>
  
  <p>I was looking for GATK best practices (like <a href="https://software.broadinstitute.org/gatk/best-practices/mutect2.php" rel="nofollow noreferrer">this</a>) but it seems it is not yet ready for production. Which alternative tools do you suggest?</p>
  
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-12-13T17:59:15.807Z
Comments.Text: Have you looked at this question? https://bioinformatics.stackexchange.com/questions/2744/somatic-tumor-only-variant-calling
Comments.UserDisplayName: Bioathlete
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-12-13T18:09:14.893Z
Comments.Text: @Bioathlete thanks, I actually didn't find that question before. However, I found that question too specific on tumor-only samples. I also have normals so maybe there are better tools?
Comments.UserDisplayName: gc5
Tags: <wgs><mutations><somatic><non-coding>
Title: Which tools are available to call somatic mutations on non-coding regions from whole genome sequencing data?
ThreadText: # Which tools are available to call somatic mutations on non-coding regions from whole genome sequencing data?
  
  (Asked by: username_0 on 2017-12-13)
  
  I have a set of whole genome sequencing samples, some of which have matched normal while some not. I want to call somatic mutations on non-coding regions.
  
  I was looking for GATK best practices (like [this](https://software.broadinstitute.org/gatk/best-practices/mutect2.php)) but it seems it is not yet ready for production. Which alternative tools do you suggest?
  
  **Tags:** wgs, mutations, somatic, non-coding
  
  > **Comments:**
  > **username_1**: Have you looked at this question? https://bioinformatics.stackexchange.com/questions/2744/somatic-tumor-only-variant-calling  
  > **username_0**: @username_1 thanks, I actually didn't find that question before. However, I found that question too specific on tumor-only samples. I also have normals so maybe there are better tools?  
  
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  ## 1 answers
  
  ### Answer by username_1 on 2017-12-13. Score: 1 | Accepted answer
  
  Those will have to be treated as separate analysis. You can use Mutect or VarScan for the matched samples and the tools listed in the [other question](https://bioinformatics.stackexchange.com/questions/2744/somatic-tumor-only-variant-calling) for the unmatched samples however that means that you won't be able to compare the results easily. If the inter-sample comparison is important you will have to run all samples as unmatched. Personally I have used LoFreq for somatic variant detection with some success. It is very sensitive so the false positive rate can be high depending on how noisy your data is.
  
  
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